Hi ,


Here is the solution for each of your queris. Mark it Solution if it fits your needs. 

1.Add check boxes to a list of records,
A check box in the heading , when the header check box is cheked all the check boxes in the list are check and vice versa.

You need to create a Wrapper Class indeed ! It will show a list of records wherin you can add a column to show a checkbox with all of the records. You need to have a select all checkbox also as per the requirement you mentioned.
For creating a select all checkbox , you need to write a small script like that mentioned in these blog 1 and blog 2. 

2.Create a site for a visual force page and change the position of the controls in page with site template.

I assume you mean to create a Force.com Site Page and not a complete Site.com functionality.
If Yes, then follow this process.

1. Click Sites and register your domain.
2. Create one Site Page and assign the Visualforce Page to it with suitable permissions.

Also , " change the position of the controls in page with site template." this line went over my mind. Please elaborate..

3.Download data thru apex in excel format.

I have done the process either way .. ie.. updated Salesforce Records via Excel. Check my blog here, if you are into re-engineering the flow and finding a suitable process for you.

If you are into apex2excel check this beautiful blog and video in which you collect your data into apex controller and give it a view via Visualforce and Get Data in Excel. 

Conceptually, you can use the contenttype attribute in the <apex:page> to convert any visualforce page render as Excel contenttype="application/vnd.ms-excel#MyFile.xls;charset=UTF-8 .

All you have to do is format the data in visualforce page as per your criteria using apex and then render the page as excel sheet using the content type attribute. Click here for more details.

Hope this fulfills your requirement. 

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