The beauty of an LED controller is that it's controlled by software (usually via USB port). Most FE's have plugins to support LED controllers like the PACDrive.
Not sure what FE you use, but the PluginLCD for GameEx will light your buttons correctly for NeoGeo games. I have my button layout the same, and just added an entry for "neogeo" in my ctrlr file and the plugin takes care of the rest.
Attached is the ctrlr file I use. In mame.ini next to the "ctrlr" entry just place IPAC2 and it will use it.