Hi ,
Your problem is not related to Atomic.
For the Samples, be sure that your samples file which is in the MAME\Samples directory has exactly the same name than the rom file. and it should work.
To enable cheat , it is a MAME configuration too. Atomic has no specific options for emulators , it only run game according to your emulator configuration.
I don't use cheat for MAME , but i know others do .(including Atomic Users). If nobody answer here , i suggest you do another post asking "How to enable cheat with MAME" or may be better do a search on the forums i bet there should be already the answer.
Hope it helps.