Since different games require different controls for these emulators, it's best to setup individually. There are ways of setting them up though if don't wanna go through that process. You can setup one game and then copy that file to all the roms you wish to have input for (i.e. Say you setup Behind Enemy Lines, after configuring that rom just copy the bel.input file to all the other rom's input files in the cfg directory). Could also just map the keys using GameEx's Advanced Config Editor and map your keys to the default ones used in the emulator. Bare in mind that it will all require tweaking for different roms but should at least save you from doing each individually.