I've made a total of three panels, and have found the 1/4 lexan to be the *only* way to go, especially with what you are planning.
My first panel used 1/8 lexan and I had to drill three lexan panels before it worked correctly. The problem was that when I would drill out the 6 buttons that close together, the panel would lose strength and shatter (one time during drilling my last button, argh!).
I bumped up to 1/4 and it was so much stronger and easier to handle. The only downside is it took longer to drill through, and, of course, was a little more expensive. I also thought that it looked and felt much sturdier/stronger/better when I was done with it. I also didn't have any fears of it cracking when people were really hammering the buttons playing a game, I was always worrying about that happening with the 1/8 lexan.
As far as the trackball, I used the normal but I'm sure it is just a personal preference