Two installs of both Mame and Mamewah. Mame and Mamewah store everything via ini's, and don't store anything in the registry. You can have two installs on one machine and the settings won't conflict with eachother.
Speaking of this though, it would be a cool feature in a front end if you could define a root folder for mame executables, and then drop multiple versions of Mame executables in there. Then in the FE, you could assign a specific version of Mame to different games, and it would run the game with the assigned version.