I am wrestling with this too. I put NES,SNES,N64, and GC ports on the side of my control panel.
The plastic hooks from Harbor Frieght would work but they are ugly and make your system look cluttered.
I would recommend a hidden compartment for the controllers above or below the coin box. Alternatively, a self on top or behind the cab.
Install the ports on the side of the CP or near the coin drawer.