I hope that I do not have recreate all my pages into the new templates.
I don't think you will have to... I would back up your site --- just in case --- and then give this a try.
Close all open documents in Dreamweaver. Run a site-wide search and replace for
<!-- InstanceBegin template="/Templates/fixed.dwt" codeOutsideHTMLIsLocked="false" -->
and replace it with
<!-- InstanceBegin template="/Templates/unlaffiliate.dwt" codeOutsideHTMLIsLocked="false" -->
After this replaces the template references, run Modify>Templates>Update Pages to convert the fixed template pages to unlaffiliate template pages. You may get notices about regions missing between pages.
After all your pages have been upated --- you may need to run 2 search & replace operations: one for the siteheader, and one to add in the affiliate.css.
Run a sitewide search & replace for the siteheader.shtml reference to point to your own affiliate siteheader file.
Then run a sitewide search and replace to add in the affiliate css reference within the head of the documents.
For both replacements you will need to open one of the (previously fixed template) documents to determine the appropriate code to search&replace for - this could be differenct for everyone using the affiliates template.