It's going to differ between people. Different arm lengths, hand sizes, enthusiasm...
This is going to sound silly, but it works.
If you have your trackball placement already decided, drill only the trackball hole and mount the trackball. Then place some vertical objects-- shampoo bottles, whatever, something that won't smash your fingers when you whack it. Then whale on your trackball like you're playing Marble Madness and Golden Tee. It's even better if you've got the trackball hooked up and working in one of those games.
If you knock something over, then that's a bad spot.
My joysticks are no closer than 6 1/2 inches, and they're only on the sides. Between the trackball and the glass I have a single button, then the spinner. The spinner is short enough to easily clear it, but if you're flinging your hand that far you're likely to bump your hand into the glass anyway.
Another thing that has helped me a lot was an extension at the center of my panel's upper tier, meant for the trackball. The bottom half of the trackball juts out (pics in my sig thread). If you drew a line horizontally across the trackball, that line would line up with the bottom edge of the rest of the panel.