Yep.
The only thing that you need to be concerned with beyond that is consistency.
Make sure that the same wires are Up/Down/etc... on ALL your joysticks.
Even more importantly, make sure that GND is the same on ALL your cables.
That way if you accidentally, or intentionally, swap the cables, GND will be the same in all the jacks.
I would recommend having four dedicated jacks (P1 Joystick/P1 Buttons/P2 Joystick/P2 Buttons).
That will allow you to plug stuff in with a minimum of hassle.
I would also recommend having a USB hub inside the CP area for trackballs, spinners, steering wheels, etc...
Those can all be swappable at the optics, or at the hub.
I actually have both in my CP.
I can unplug the mouse hack from the USB hub, disconnect whatever is hooked to it by removing the Cat-5 cable, connect a new device, and plug the USB cable back in.