Bit late but anyways...
I have two seperate files, one for the homepage and one as a general template. This is because my homepage has lots of little boxes and so I need a slightly different style template to add content to a main box in the middle. So thats how I use the design as a dwt, you can find see what I mean on my site.
Also, I have another template from alance that was coded into php, which works great. So all the navigation is in seperate files which updates all of the pages if I update one link. I think this is what you are looking for, and alance can do it for you for a small charge.
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