Yes, Body putty. Wood putty tends to be harder to use and is harder to sand.
There's no issues with your control panel overlay sticking to the mounting plate, wood, body filler, wood putty. The real issue is you want to have a smooth finish so there's no evidence of a trackball mounting plate. If you did not cover the plate with anything all of the plates imperfections would be quite obvious through the overlay.
I have completed a DIY tutorial w/pics on this subject. I will e-mail it to you tonight after I get home from the day job.
Jack