I've had Canon cameras going back to the 70's and the Canon EOS Digital Rebel XT is the hardest one I've ever seen to use. I think this is because it is designed for total beginners, so it tries to automate everything and that makes it harder to use for anything but automatic. You have to use the manual on this camera. Which is amazing, because you can take the 20D and without even cracking the book know how to do most of what you need to do (unless you get fooled by having two On positions and only us the first).
On the matter of folders, this seems to be a consistent pattern with Canon dSLRs. I believe the 5D and the higher end gives you more control of folders. I suspect that the techies that came up with this idea has some real world reason for doing it, but they never shared it with me.
I use Downloader Pro to move the photos off the card to the hard drive. It treats the card as a single unit, so you never even see the folders. It has so many fantastic features to automate your CF downloads that you might want to check it out ( http://breezesys.com/Downloader/index.htm
I set it up in a fully automated mode, so as soon as the card is put in the CF card reader it starts copying the photos off and into an appropriate folder that it automatically creates per my instructions.