So after 2 days of searching here is my result,

PLEASE LET ME KNOW IF IT HELPS YOU

FEEL FREE TO POST AN UPDATED CODE

You can do this with ORGs that can have Apex Classes (sorry Professional i tried so much but i could not make it work, not the Save Pdf File part).

So follow this steps and you will get something cool.

1) Create your Apex VF page with the Standard Controller "Quote" and RenderAs="pdf".  Mine is called "Prueba_PDF"

2) Create a WebService as follow (could be a Controller too) :

global class AttachmentGenerator {
   webService static String AttachPDFToQuote(string Id) {
        string retRes = '';
        try
        {
         PageReference pageRef = new PageReference('/apex/Prueba_PDF?Id='+Id);
         Blob content = pageRef.getContent();
         QuoteDocument doc = new QuoteDocument(Document = content, QuoteId = Id);
         insert doc;

         retRes='SUCCESS';
         return retRes;
       } catch(exception ex) {
           System.debug('--- Error ----------'+ ex);
           retRes= ex.getMessage();
           return retRes;
       }
   }
}

3) Create a javascript file mine is called "QuoteCustomWS.js", here you are going to call the WebService:

function SaveQuotePDF(a) {
    try {
        var res = sforce.apex.execute("AttachmentGenerator","AttachPDFToQuote",{Id : a});
        if(res=='SUCCESS')
            window.location.reload();
        else
            alert('Error in attaching file ----'+ res);
    } catch(er) {
        alert(er);
    }
}

4) Upload this File as a Static Resource and then click view and copy the URL without the namespace.  For example "/resource/1350609029999/QuoteCustomWS" .

5) The last ,but not least, very important thing, create a Custom Button in Quotes that executes javascript (OnClick Javscript):

{!REQUIRESCRIPT("/soap/ajax/24.0/connection.js")}
{!REQUIRESCRIPT("/soap/ajax/24.0/apex.js")}
{!REQUIRESCRIPT("/resource/1350609029999/QuoteCustomWS")}

var pdfOverlay = QuotePDFPreview.quotePDFObjs['quotePDFOverlay'];
pdfOverlay.dialog.buttonContents = '<input value=\"Guardar Presupuesto\"  class=\"btn\" name=\"save\" onclick=\"SaveQuotePDF(\'{!Quote.Id}\');\" title=\"Guardar en Presupuesto\" type=\"button\" /><input value=\"Cancelar\"  class=\"btn\" name=\"cancel\" onclick=\"QuotePDFPreview.getQuotePDFObject(\'quotePDFOverlay\').close();\" title=\"Cancelar\" type=\"button\" />';

pdfOverlay.setSavable(true);
pdfOverlay.setPDFContents('/apex/Prueba_PDF?id={!Quote.Id}',null,null);
pdfOverlay.display();

6) Add the button to your Quote Page Format.

Important things to consider:

a) The Code in the Custom Button is use to View the File in the "Salesforce PDF Viewer" but it will not be complete without the "Guardar Presupuesto" button that calls the WebService using the "QuoteCustomWS.js".  You need all the code to make this work.

b) If you want different Templates you could just add a Picklist Custom Field to your Page Format and add the names of them.  Then grab this info in the Custom Button and change a little but the "QuoteCustomWS.js" to grab the name of the Apex VF Page to save. Easy.

I tried so hard with Professional edition and i did not make it work, not the Save Pdf file Part thats actually on the Server side.  If someone could just read the Embed PDF with Javascript let me know, thats the part that i could not do.  If we could complete this, we could all use this great feature as we please.

Cheers and thanks for reading.