I think I'm getting close to figuring out a system for getting my art to look the way I like in the game. I'm starting out with real loose sketches that I scan into the computer. Then I import them into Toonboom (any coloring software would work) and trace the image. I prefer Toonboom only because I can tinker with the palettes quickly without having to refill everything in. Then I take the art into Photoshop, use "Save for Web" in the File menu, shrink the image, and then start limiting the palette. In the past, I would just drop the colors to a max number and see what photoshop gave me. Now I'll take it down to 64 or 32 and then start deleting the colors that I don't want. The program will compensate with pleasing results. I'm trying to achieve a sort of classic Lucasarts/16-bit/Arcade look for my game, so these extreme measures might not work for you. I'll probably still have to go into the final art and delete a block here or there, but after I save each character's distinct palette, I should be pretty close. If the "Save for Web" feature has one draw back, its that the "undo" function doesn't really work there. So if you delete a color and realize you didn't want to, you're kind of out of luck. It happened to me when I accidentally deleted the transparent channel.
In other news, the previous hiccup in my 3D Buzz XNA studies is already over thanks to the help of their community. Turns out I had placed some temporary code in the program in order for it to stop returning errors. I hadn't corrected it by the end and it kind of bit me in the ass. I'll be sure to stick around their forums as the users there were quick to help me get past a very "noob" mistake.