You need to make sure to have an atom.opt in your config/mame/ folder. mine looks like this…
mame_alternate_renderer = "disabled"
mame_altres = "640x480"
mame_auto_save = "disabled"
mame_boot_from_cli = "enabled"
mame_boot_to_bios = "disabled"
mame_boot_to_osd = "disabled"
mame_buttons_profiles = "enabled"
mame_cheats_enable = "disabled"
mame_cpu_overclock = "default"
mame_lightgun_mode = "none"
mame_mame_4way_enable = "disabled"
mame_mame_paths_enable = "disabled"
mame_media_type = "rom"
mame_mouse_enable = "enabled"
mame_read_config = "disabled"
mame_saves = "game"
mame_softlists_auto_media = "disabled"
mame_softlists_enable = "disabled"
mame_throttle = "disabled"
mame_write_config = "disabled"
My command line looks like this…
E:\RetroArch\retroarch.exe -L "E:\RetroArch\cores\mame_libretro.dll" "atom -rompath "E:\Temp\atom" -flop1 "E:\Temp\atom\galxians.zip" -autoboot_delay "2" -autoboot_command "*dos\n*dir\n*cat\n*run"galaxi"\n`
the non-paired quote before the driver name "atom
is needed in all of my command lines… I have no idea why. You can try it without and see if it works for you. I get a failed path error in my verbose log when I do.
The last part…
*run"galaxi"
can be found in the system/mame/hash/atom_flop.xml
it is diferrent for each game.
After you get it to run this way then, in your atom.opt…
if you use…
mame_read_config = “enabled”
and temporarily have…
mame_write_config = “enabled”
It will write the rompath to an ini file. Turn off write config once you verify the ini contents.
Now you can eliminate the rompath from your command line. 
There is a method used on Android where you strip the command line down to…
atom -rompath "E:\Temp\atom" -flop1 "E:\Temp\atom\galxians.zip" -autoboot_delay "2" -autoboot_command "*dos\n*dir\n*cat\n*run"galaxi"\n`
and use it as the contents of a *.cmd. (In this case I would name it galxians.cmd)
This can be loaded as content by the MAME core like a rom. I have gotten the method to work with the Alice32
and bbcb
but I have been having issues with other systems. It may just not work well on Windows.