Different ways (depends on used emulator, that you didn't told us

):
>
create .iso files:
it "combines" cue and bin to one single file.
but depends on used emulator. or that any conversion tools supports it.
please tell us which emulator..
>
add multiple rom file extensions to AM and edit/clean your romlist afterthen manually:
if this are your romfiles:
game1_1.bin
game1_2.bin
game1.cue
game2.bin
game3.bin
-set multiple file extension and create collection/romlist in AM:
executable C:\attract\your_emulator\your_emulator.exe
args "[romfilename]"
rompath C:\attract\your_emulator\ROMS
romext
.cue;.bin-then open your romlist, remove unnecessary entries and save it
here:
C:\attract\romlists\your_emulator.txt
remove:
game1_1.bin
game1_2.bin