Hi Bogdan Kulyk,
Subtotal__c and Non_Pick_Total__c are Roll up summary fields on Opportunity Object. They give the "Sum" of Opportunity Product aggregates on Extension Field.
Non_Pick_Total__c --Data Type Roll-Up Summary Summary Type SUM
                              Summarized Object Opportunity Product    
                            Field to Aggregate Opportunity Product: Extension
                          Filter Criteria PickEQUALSFalse

Similarly for Pick Total :Data Type Roll-Up Summary Summary Type SUM
                                 Summarized Object Opportunity Product    
                                   Field to Aggregate Opportunity Product: Extension
                                  Filter Criteria PickEQUALS TRUE
Subtotal :Data Type Roll-Up Summary Summary Type SUM
               Summarized Object Opportunity Product    
                Field to Aggregate Opportunity Product: Extension
                Filter Criteria

Controller :

public with sharing class InvoiceController {
           List<wrapperClass> appointmentList {get;set;}
           List<wrapperClass> appointmentList1 {get;set;} 
           public list<string> address{get;set;}
           public string address1{get;set;}
           public string address2{get;set;}
           public string address3{get;set;}
           public string address4{get;set;}
           public string address5{get;set;}
           public string address6{get;set;}
           public string address7{get;set;}
           public String showaddressonVf{get;set;}
           public string wholeaddress{get;set;}
            public static wrapperClass tempObj2 ;

   //Added by sumit
               List<String> stringList ;
               public String all{get;set;}
           //------------
   public InvoiceController(){
   list<opportunity> op=[select id,Shipment_Info__c
   from opportunity where id=:apexpages.currentpage().getparameters().get('id')];
    //opportunity op=[select id,Shipment_Info__c from opportunity where id=:apexpages.currentpage().getparameters().get('id')];
       //---------------------Added by sumit----------------------
       stringList= new List<String>(); 
       if(op.size()>0)
       if(op[0].Shipment_Info__c!=NULL && op[0].Shipment_Info__c!=''){
           List<String> stringList=(op[0].Shipment_Info__c).split(',');
               for(integer i=0;i<stringList.size();i++){
                   all=all+stringList[i]+'<br/>';
               }
           
           all=all.remove('null');      
        }
      //------------------------------------------------------------
   }
       public Id OppId{get;set;}
   
       
    
       public InvoiceController(ApexPages.StandardController sc) {
       oppId=Apexpages.currentPage().getparameters().get('Id');
   }
               public List<wrapperClass> getappointmentList (){
               wrapperClass tempObj;
               tempObj = new wrapperClass();
        
               List<wrapperClass> aReList = new List<wrapperClass>(); 
           List<Opportunity> opp=[select id,Name,AccountId from Opportunity where id=:oppid limit 1];
           List<opportunity> Opp1=[select id,name,CreatedDate from opportunity where id=:oppid];
           //Opportunity opp1=[select id,Name,AccountId from Opportunity where id=:oppid limit 1];
           //Opportunity Opp=[select id,name,CreatedDate from opportunity where id=:oppid ];
                          List<OpportunityLineItem> OPplineitem= [SELECT OpportunityId,Quantity,PricebookEntry.Product2.Name,Sys_total_Amount__c,LN__c,Extension__c,ListPrice
                          ,Pick__c,Schedule_Ship_date__c,Bin_Item_Code__c ,PricebookEntry.Product2.Product_Line__c,OpportunityLineItem.Opportunity.Subtotal__c,OpportunityLineItem.Opportunity.Non_Pick_Total__c
                           FROM OpportunityLineItem where OpportunityId=:oppId]; 
                          system.debug('HHHHHHHHHH'+OPplineitem.size());
                          tempObj2 =new wrapperClass();
                         // tempObj1.Subtotal=
                       for(integer i=0; i < OPplineitem.size(); i++)
                       {
                     tempObj = new wrapperClass();
                     tempObj.productname= OPplineitem[i].PricebookEntry.Product2.Name;
                     tempObj.BinItemCode=OPplineitem[i].Bin_Item_Code__c;
                     tempObj.quantity=OPplineitem[i].Quantity;
                     tempObj.totalamount=OPplineitem[i].Sys_total_Amount__c;
                    // tempObj.Subtotal =OPplineitem[i].Opportunity.Subtotal__c;
                 //   tempObj.NonPickTotal=OPplineitem[i].Opportunity.Non_Pick_Total__c;

                     //j=j+OPplineitem[i].Quantity * tempObj.unitprice;

                    // tempObj.productline=OPplineitem[i].PricebookEntry.Product2.Product_Line__c;
                     //Add a conditional statement here
                
                
                 if(OPplineitem[i].PricebookEntry.Product2.Product_Line__c=='DIE') 
                     {
                      tempObj.unitprice=0.01;
                      tempobj.extension=OPplineitem[i].Quantity * tempObj.unitprice;
                      tempObj.productname=OPplineitem[i].Bin_Item_Code__c;
                      //tempObj.Subtotal =j;
                      if(i==0){
                      tempObj2.Subtotal=tempobj.extension;
                     }
                     else{
                      tempObj2.Subtotal=tempObj2.Subtotal+tempObj.extension;
                       }
                    
                    // tempObj1.Subtotal =tempObj1.Subtotal+tempObj.extension;
                     system.debug('@@@@@@@@'+tempObj2.Subtotal);

                    //tempObj.NonPickTotal=OPplineitem[i].Opportunity.Non_Pick_Total__c*tempObj.unitprice;
                      
                     }
                 else
                     {
                     tempObj.unitprice=1;
                     //tempObj.unitprice=OPplineitem[i].ListPrice;
                     tempobj.extension=OPplineitem[i].Extension__c ;
                    }
                     tempobj.LineNumber=OPplineitem[i].LN__c;
                     tempobj.Pick= OPplineitem[i].Pick__c;
                     tempobj.ScheduledShipDate = Opplineitem[i].schedule_ship_date__c;
                     
                     if(tempobj!=null){
                        aReList.add(tempObj);
                     }
                    }
                   
           return aReList;
           
           
   }
   
   
  
       public List<wrapperClass> getappointmentList1 (){
           wrapperClass tempObj1 ; 
           List<wrapperClass> aReList1 = new List<wrapperClass>();
                   List<Opportunity> opp=[select id,Name,AccountId,Shipment_Info__c,
                    Shipping_Address_Line1__c,
                        Shipping_Address_Line2__c,
                        Shipping_Address_Line3__c,
                        Shipping_City__c,
                        Shipping_State_Province__c,
                        Shipping_Zipcode__c,
                        Shipping_Country__c  
                        from Opportunity where id=:oppid];
           for(integer i=0; i < opp.size(); i++)
           {
             tempObj1 = new wrapperClass();
             tempObj1.billingAddress= opp[i].Shipment_Info__c;
                               }
             aReList1.add(tempObj1);        

             /* Below code commented by Kiranmai as Shipment Info field is split into multiple fields
             
             //------- Added by Sumit-----------  
             stringList= new List<String>(); 
                  
             if(aReList1[0].billingAddress!=NULL && aReList1[0].billingAddress!=''){
                List<String> stringList=(aReList1[0].billingAddress).split(',');
                for(integer i=0;i<stringList.size();i++){
                   all=all+stringList[i]+'<br/>';
                }
             } */
               
             all = all + opp[0].Shipping_Address_Line1__c + '<br/>';
             if(opp[0].Shipping_Address_Line2__c!=NULL && opp[0].Shipping_Address_Line2__c!=''){
                 all = all + opp[0].Shipping_Address_Line2__c + '<br/>';
             }
             
             if(opp[0].Shipping_Address_Line3__c!=NULL && opp[0].Shipping_Address_Line3__c!=''){
                 all = all + opp[0].Shipping_Address_Line3__c + '<br/>';
             } 
              
             if(opp[0].Shipping_City__c!=NULL && opp[0].Shipping_City__c!=''){
                 all = all + opp[0].Shipping_City__c + '<br/>';
             }
             
             if(opp[0].Shipping_State_Province__c!=NULL && opp[0].Shipping_State_Province__c!=''){
                 all = all + opp[0].Shipping_State_Province__c + '<br/>';
             }  
                 
             if(opp[0].Shipping_Zipcode__c!=NULL && opp[0].Shipping_Zipcode__c!=''){
                 all = all + opp[0].Shipping_Zipcode__c + '<br/>';
             }
             
             if(opp[0].Shipping_Country__c!=NULL && opp[0].Shipping_Country__c!=''){
                 all = all + opp[0].Shipping_Country__c + '<br/>';
             }
            /* all = all + opp[0].Shipping_City__c + ', '+opp[0].Shipping_State_Province__c + ' - ' + opp[0].Shipping_Zipcode__c + '<br/>';
             all = all + opp[0].Shipping_Country__c + '<br/>';*/

             all=all.remove('null');
                     
                /*-----------------------------------*/ 
      return aReList1;  
   }
           public class wrapperClass{
          // public String Item{get;private set;}
           public String productname{get; set;}
           public String BinItemCode{get;set;}
           public Decimal Quantity{get;set;}
           public Decimal totalamount{get;set;}
           public Decimal Subtotal{get;set;}
           public Decimal NonPickTotal{get;set;}                            
           public Decimal unitprice{get;set;}
           public date todaysdate{get;set;}
           public decimal extension{get;set;}
           public string LineNumber{get;set;}
           public string billingAddress{get;set;}
           public string splittedaddress{get;set;}
           public string productline{get;set;}
           public string wholeaddress{get;set;}
           public boolean Pick{get;set;}
           public date ScheduledShipDate{get;set;}
           public wrapperClass(){}                
       }
       
      
}

This is the complete controller .
Now Based on the Condition
Condition 1:

If the product line for the product selected in opportunity items is ‘DIE’ make following changes .

1) unit price should change to $.01. // Condition Works

2)Unit price just change on the PDF display only and with extended amount which will be quantity times .01.

  Extension = Quantity*0.01 // Condition Works
3)productname =BinItemcode // Condition Works
4)Subtotal = NonPickTotal //Condition doesnot work -------Here the value should change as per the logic written and display on the vf page the total should be 11 but its reflecting as 1100.



Condition 2:

If the product line for the product selected in opportunity items is '!DIE’ make following changes .

1) unit price should change to $1.

2)Extension =Extension

Any help very much appreciated.