Once again, it's personal preference.
That said, most people use the trackball with their right hand with buttons on the left. As far as I know most arcade games that used the trackball are set up this way as well. Missile command definitely is set up this way.
Yup, right hand TB was the most common, AFAIR. Rampart manual has the buttons on the left, too.
The Cabal convertion manual shows putting two buttons on each side, but suggests only to do that "If you player base demands it and you have enough room." Otherwise it doesn't recommend which side of the trackball.
OTOH, if the CP had only one TB in the middle, it almost always had buttons on both sides.
I usually use right TB, left button arangement, but doing this, I was weaker/slower pushing the ball to the right, especially down right. So sometime, if the CP had buttons on both sides and the game demanded heavy right at some point in the game, I'd switch to left TB, right buttons for that section of the game.