Creating two directories in /Users/yourname/Library/Application Support/ with slightly different names and just changing the name to the one recognized by the application works, however, this takes too much time. Is there an easier way to change between versions of an application? For example, somehow editing how the application recognizes which directory to write to and having a shortcut to the original and edited version of the application.
Keyboard Maestro can do this by running a macro upon application launch/quit.
Have your two folders for your application named such as '<app name>-main' and '<app name>-second' then switch them out using macros such as the following:
Or you could even try creating another user to just run that App. It would give you another "~/USERNAME/Library/Application Support" folder.
Depending on your available memory, etc. this might even be quicker and less of a hack (hence potentially fewer issues).
Of course that assumes that the application keeps ALL of it's information in the user's library folder and not the one for the whole system...