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So as not to adversely SE rankings I plan to keep all file names the same (plus there is no real reason to change them).
Of course, if you have several different parts to a website, it's possible to use more than one template...
I don't know if it's best to develop the new site in a subweb and then, once the site is ready for publication, overwrite the current site. Or perhaps use some other method.
I'm basically doing that now. When all is ready I'm going to wipe everything off the server to make sure that all the old bits and pieces are gone. Then simply publish newweb to the server.
treeline's idea of using a test domain first something I'm now definitely going to do.
When I am going to redesign a site, I first do the design in a layout program. For me, the absolute best program every invented for this is OmniGraffle by OmniGroup. It is kind of like Visio fr Mac OSX but is just so much more powerful. You can drag and drop anything, sping things, drop shadows, etc.
Anyway, so I come up with a design on that, then take that and write it out in XHTML/CSS using a text tool (BBEdit, UltraEdit, etc) to make sure it works in all browsers.
Then, since I am using a template driven website, I upload the new images and modify the main templates (for me, just standard_html_header and standard_html_footer) as well as drop in the new CSS. That is 95% of the work.
If the site is designed well and uses the right elements, everything works. Of course, you always find a few issues, but I post news items to tell users that a new design is coming (maybe post a PDF of the design in advance) and ask for feedback or if they find bugs. I have found that most users love looking a new things and helping out.