I kept it simple for my friend. We put external USB ports on the outside, too, but he had issues when he'd swap, and didn't want to call me every time for support. In the end, he wanted to go simple, so we went that route. We were going to use ControllerRemap, but it was way simpler for the both of us to just leave everything plugged in. He even put a pair of AimTraks in there, as well.
Personally, it's an arcade cabinet, not a console emulator, so I wouldn't have even used those external controllers, but it's his cabinet. He's happy now.
