This sure sounds like you just need to configure the controls in the actual emulators. Since the emulator is included in the pnp module, it may be configured in a way that is not compatible (at least initially) with your setup. Try setting up the controls manually:
PS1Run <AtomicFE Dir>\plugnplay\psx\psxfin.exe
Click on File, then Configuration.
Click on the Controllers Tab
Configure each control the way you would like it.
Click OK, then Exit
N64Run <AtomicFE Dir>\plugnplay\nintendo64\Project64.exe
Click on Options, Controller Plugin
Define your controls, Click OK
Click File, then Exit.
SNESRun Run <AtomicFE Dir>\plugnplay\snes\zsnesw.exe
Click on Config, Input #1
Choose Keyb\Gamepad
Click on each control, define it
Close Input #1, repeat for other inputs
Close zsnesw
Good luck!
