no, that's fine, i guess it all depends on how you have it setup. If he needs to use seperate settings for the emulators, then yeah, he will probably want to upgrade.
If you don't want to upgrade, you have 2 options:
1) configure all your emulators to use the same keys, and just start joy2key prior to mamewah launching
or
2) use .bat files for the actual emulators, instead of launching the emulator executable, launch a bat file that will start joy2key with the emulator configuration, and then start the emulator. I think with joy2key, it does not start a seperate application.
I double checked it and it doesn't start a seperate joytokey application, so you can run it over and over when launching your emulators.