It's ok :) Everyone has/had done this before.. ;) I made up an image that might help you understand a little better ok..?
Well, hopefully it's not confusing.. =P
http://www.vindictivebastard.net/images2/themeplacement.gif
However, *some* themes place their style.css sheets in other places.. like, instead of being in with the other PHP files, like in that Image of mine there... they sometimes put it in a folder called "stylesheets" or something..
Like:
--default <-- Main theme folder
-----images <--inside main theme folder, for images.
-----stylesheet <--inside main theme folder, for CSS files.
------ All other PHP files..
But, maybe just check my image once and see if that might help first. =)
spencerp