I have these buttons specifically mapped on my X-Box 360 controller with joy2key:
up: 1
right: 2
down: 3
left: 4
RT+up: 5
RT+right: 6
RT+down: 7
RT+left: 8
LT: 9
back: 0
start: F12 (menu)
RB+start: F2 (equip)
RT+start: enter (for lazy game creation with gamepad)
Left Joystick press-in button: a (for breaking out of ice fast)
Right Joystick press-in button: d (for breaking out of ice fast)
RB + up/right/down/left = unmapped (so I can hold RB to break out of ice without triggering my number bar by accident)
Everything else is mapped like normal (I got "back" and "start" unmapped so I could use joy2key by using an external program to set them to nonexistant buttons 14 and 15 - xbox controller only goes up to button 10)
I also use Tofuman's palette manager to map multiple palettes (and run 2 instances of it for a total of 8 palettes):
RB+D-pad-up: L-shift+1
RB+D-pad-right: L-shift+2
RB+D-pad-down: L-shift+3
RB+D-pad-left: L-shift+4
RT+D-pad-up: R-shift+1
RT+D-pad-right: R-shift+2
RT+D-pad-down: R-shift+3
RT+D-pad-left: R-shift+4
I chose "shift" as the key for palette manager because shift+number doesn't trigger the number bar in game.
I also use the second row for the number bar, since I use palette manager. My 0 key (back button) is moon atomizer on all characters, and my RB+0 key is ryuker. And then I use RB+5678 (RB+RT+up/right/down/left) to map extra keys if needed. I don't use RB+1234 because that would conflict with my "breaking out of ice" strat. I also don't remap 9 (LT) because it's my panic resta button.
I have also modified my joystick deadzones in joy2key to 45%, so I only press the wrong direction if I'm REALLY not paying attention. It's actually pretty easy, even when I'm using it to cast techs on a FO.