MP 360 overheats no matter what i do

Do you have 'vacuum advance' set up in the unit?
If not, you could leave Base Timing at 15° and add, say 8° of vacuum advance.

I'm reading and educating myself on a different screen on how to program the Atomic and also noticed one has to setup the distributor and rotor with 15° advance. I think there's also a part of 'rotor phasing' being done here.
In doing so you need to put the Atomic in Lock timing mode so you confirm actual timing.
After that you need to Unlock timing again so Atomic can actually control timing again. Has this been done?