Haha! I really don't think I'm the one to help you, I use Photoshop and all I know about it is what I learned in the one computer art class I took in High School.
I only ever use Jewel cases when I absolutely can't find the original boxes though, some of my games I still had the original boxes for others I had to buy again or borrow from people I know. Since the boxes are already Rectangles like DVD cases they usually don't get distorted noticeably.
As far as cutting the name of the game to fit the spine or other graphics I might need, I get a lot of use out of the magic wand tool, and magnetic lasso.
So yeah, I'm really not that good at this stuff. You should ask Sheep2001 since he's the new CoverGuru and all, haha.
*edit* Just read Doom's post, good guy that Doom.