I just wrote that in my project announcement thread I think.
Honestly, I dont think that there's necessarily a right or wrong way to go. I top mounted them mainly because I didnt want to have any bolts or screws showing through the overlay (but then ended up having them anyway when my Lexan started lifting). Also, I liked the idea of having some wood underneath the joystick to support it rather than just the bolts and nuts holding them up. Finally, and this may sound like a terrible reason, I really like the work that Knievel does, and he does it that way. Since he's a cab building God, I figured I could do much worse than following his lead.
Bottom mounting would have made it easier to swap out the sticks if I ever needed to, but I also ended up not using the adhesive on my CPO, so it wouldnt be that hard to get to them either if I ever needed to. Either way you almost have to rout out an area to sink your mounting plate to, so its not much different. One benefit of bottom mounting is that you do plan on using the adhesive from your CPO, you dont have to cover up the routed area with bondo or cardboard or anything.
As for the trackball, I think you have to topmount them unless you plan on not using the mounting plate and bolting the TB directly to the CP. I didnt feel comfortable doing that considering how hard I generally hit the trackball playing Golden Tee. Also, I think you'd end up doing just as much routing and cutting, if not more, to get the TB at the right height if you dont use the mounting plate. I remember reading a thread somewhere where a couple of people have done it, but I didnt feel comfortable going that route.