Hi,
I think you can use some tools to classify your roms. like clrmame may be to do that.
Tools based on the control.ini file for instance.
If you want just generate a list of game using 4 ways joystick and then copy it by hand. You can use the AtomicManager tools (provided with AtomicFe). On the "Game list" tab (it appears if you check "use game list" on the "advanced tab" , you can select "Control.ini" on the combobox then on the second one select "Joystcik 4 way". And click on "Transfer category".
But i bet others tools more specific does that too and will even copy your files.