Hi Brian,
You can use lokki's solution. Create an INI folder under your mame directory , and create a ini file which match with the name of the rom file. ex for pacman.zip , create a pacman.ini with the specific settings for your game. (if you use arcadeVGA and you used Arcade Vga Resolution tool , you should already have an INI folder with .ini for all game i think).
But if you want use Atomic to do the same kind of things.
On the "advanced tab"
in the "advanced options" section
in the ROM code combobox , select or type your rom name for which you want specific option.
then in the "command line to execute" field type your commande line to run your rom
ex : C:\mame\mame.exe pacman -ror -skip_disclaimer -skip_gameinfo
(or you can create a .BAT and call the .BAT from this commande line)
Then, Click "ADD" button.
A new row will appear in the list below , like
pacman=C:\mame\mame.exe pacman -ror -skip_disclaimer -skip_gameinfo
then click SAVE , and it shoud be ok. When Atomic will try to run pacman , it will run your specific command instead of the default config.
i hope it helps you.
Cheers.
Youki