Sounds like you shouldn't be using the betas then.
Perhaps not. But see, how can I be a user as well as a contributor if I don't get involved with the betas? If I am just a user, I can't give back to the cause, but if I do, I can't get up to speed, because of drastic changes all over.
I fail to see how that is an issue - your base_url would change both times to the correct value. If your site is in www.mydomain.com, then
the $base_url variable is "www.mydomain.com/mysite"
If I then modify base url in the theme and phptemplate as suggested, and put the path to an image in my theme as <a href="files/pictures/whatever.jpg"> then it does not obey the base url, and tries to read the file from www.mydomain.com/files/pictures/...
Where's the actual problem? What links, exactly, aren't working for you? Where is there an online demo so we can see what you're talking about?
Site at home on localhost - no live demo at the moment. Sorry :-( But I hope my elaboration makes a bit more sense now.
Kobus