The problem is that you are putting the cart before the horse. Templates are not intended to be added to documents. They are intended to be used to create new documents. Basically adding a template to an existing document will simply offer the potential of updating the styles in the document to match those similarly named styles in the template.
The headers and footers in the template are not part of the deal.
It would make more sense to copy your document content to a new document created from the template - and even then there could be issues with headers and footers especially in a document that has several sections - each of which potentially has three different header/footers.
Given that your aim is to change the headers and footers of a selection of documents, if all the documents currently have headers and footers then in order to determine how to change those headers and footers, it would be necessary to know what is in each of the header footer ranges and what you want to replace them with.
With that information available you can then produce a macro that will make the changes and if
http://www.gmayor.com/document_batch_processes.htm doesn't have a process that will work for you, you can create a process to work with it and let it handle the files.