when i was a kid and had like 5 systems hooked up in tandem, i used to have the snes jjoystick and the genesis joystick. i had velcro on the desk so i could change sticks and they'd be generally still.
however, this leaves large strips of velcro on your desk, which as a kid was no big deal, but i wouldnt do it now.
If its gonna be a semi permanant thing, maybe embed two tnuts in the desk that you can actually screw the CP down to the desk via a turn key\screw.