Took me a few minutes to figure this one out but make a separate emulator entry in LB, call it whatever you want, I used NeoGeo AES, it can point to you normal install.
In the Edit Emulator screen for that emulator entry set your default command parameters to aes and turn on "Use File Name Only". Also don't forget to add the platform name in the Associated Platforms tab.
This doesn't work because Mame expects a .bin file for it.