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If you take the template out of DW and just modify and upload that alone, then nothing will happen to the other pages.
So yea, if you know a way to create a link between the template and the other files outside of DW, then that is what you need to do.
They usually have tags inside that refer to the template.
Make sure that you keep the same file and folder distribution that the original had. Then, with your template also in the project, open and modify it.
However - the accordion does not work for all of the xhtml files.
The file only is only controlling the navigation and the head of the site.
And your guess is correct, the template modifies areas that are not specific to a page.
Usually, this is done by creating Editable Regions in the template.