Hi Mark,
this is an excellent question.
It's useful to think of CSS and JS files as being "compiled".
On the one hand it's useful to keep separate css files separate. ie the jQuery ui files, the nettalk files, your custom files - it makes sense that these are all separate from a development point of view. On the other hand, for performance reasons, it's good to combine the files into a single css file, and then compress them into a .gz file.
Think of the GzipAll.Bat file as the "compiler" in this case. (So if you change a source file, you can "recompile" by re-running GzipAll.Bat).
What you saw in your first look was "theme.css" - which is actually the "compiled" css file. So that information wasn't useful to you. Fortunately you found the "source" file, but that's more down to your persistence than anything else.
so what _could_ you have done? Well, (especially while developing styles), it's possible to run your site with "uncompiled" css files. In other words all the separate files are sent to the browser, and compression is not used. This is set in the WebServer procedure, on the Advanced tab, "combine and compress files". If you tick this _off_, then you'll be able to see the exact sources, and go from there. Once you're done, put it back on, and (crucially) re-run Gzipall.bat.
A good explanation of the order of the files, and where you slot yours in, is here;
http://www.capesoft.com/docs/NetTalk6/NetWebThemes.htmCheers
Bruce