I agree with the admin buttons (Start, Exit, Pause) being Top & center... It just makes it easier for both players to have acces to them.
I would also look at moving the 8-way joysticks & buttons up a little... You want to make sure there is plenty of room for your hands to rest on the panel for those long game nights...
I like the background you've got going, but the overlays (blue & yellow) seem a little out of place. I like the idea of overlays, but they have to mesh well with the rest of the graphics... I'm sorry I don't have more ideas on this (I don't like to put things down without a decent alternative, but I'm usually not creative enough when it comes to the whole art scene)
And I do like the characters floating around the overlays... It just looks cool.
I'd also keep the buttons next to the 4-way... It just doesn't feel right reaching around to the other buttons...
Some people like the 4-way off next to the P1 stick, but I wouldn't do that...
Just my opinion, but I like the 4-way to be as close to the center [left-to-right] of the panel as possible... Ms. PacMan just doesn't feel right when you're standing off to the left of the screen.

You trackball looks like it should be alright where it is now too... & keep the buttons if you'll be using Windows, they come in handy (even if some people don't like them... *cough* HC *cough*)
Just make sure that the panel is functional & comfortable for you. Once you've built a test panel & figured out what you like, stick with it.
My only general advice on layouts is try not to clutter up the CP too much... It'll just confuse people when they first walk up to it. Make sure your controls labled well too. Blank CPs are doubly confusing!