Totally depends on how you have your system set up. Your cab controls would be wired up to your encoder - sounds like you understand how that works. The absolute most idiot-proof way of doing what you want is with a Kade mini-console plugged into your usb on the mobo and with the DB port broken out to the cab exterior. Then you could use original controllers plugged in via adapter cord and the Kade would do all the magic.
The flip side would be getting USB versions of each controller you want and then config each emulator to use each controller. You might need to re-config each time though, like you mentioned, cause USB is retarded that way. I know there is an app out there that fixes this issue but I can never remember the name of it.