With Atomic and Mame , you don't need to rotate with Ati.
You can simply rotate Atomic by choosing Orientation "Vertical ->" or "Vertical <-" on the general tab of Atomic manager.
Then on the "folder" tab, at the end of the field "default emulator" , add -rol or -ror . For instance to have something like :
c:\mame\mame.exe -ror
Then all your game should be rotated when you run them.
If you want filter vertical game (despite the fact that with -rol you can play also horizontal game rotated).
You simple solution is to put only vertical game in your folder.
But you can also create gamelist that contains only vertical game.
To do that game list, you can use External tool like Romlister (i think there is thread somewhere here about it).
Or use build in gamelist creator in AtomicManager.
To know how it work , i strongly suggest you do step by step the "simple tutorial" i created, you can find it on Documentation page of my website.
After that you should have good base to understand and use Atomic. and create your config as you want.
Don't forget to install the last patch of atomic , if you didn't already do.
I have a official support forum in english here :
http://spaceinvaders.7.forumer.com/