I just set mine up in MALA. There was a checkbox to exchange axis. The wheel is set to x-axis, and the list is on the y-axis; it makes sense to swap them. If you don't see a way to configure it in atomic, PM youki. He is always pretty quick about helping with config questions in Atomic.
For MAME, open mame.ini with notepad. Scroll down until you see the control section. Change mouse = 0 to mouse = 1. You might be able to set this in Atomic but I don't know. I was able to in MALA.