So :

First : Install AtomicFE (Do not configure)

Then , install each module you want.

For certain modules you have may be to click on a .REG file (it is written in the installer when needed)

Copy your roms in adhoc folder

Run Atomic.Exe and Play!

PLAYER1_BUTTONSTART (or ENTER Key) to select (enter in a menu or run a game)
PLAYER2_BUTTONSTART (or BACKSPACE Key) to go back in a menu.

Keys can be configured using AtomicKeys.exe