I will try my best to help you.

So first I need some more info about your mission.

If NATO and AAF are in the same AO with the same military placements then they will spawn together.

I might know what your trying to do though, im guessing, that you want AAF in the NATO AO without them spawning in the same exact area, here is how I will fix this.

What I would do is have NATO have the Mil Objectives while AAF have Civ Objectives. This should fix your problem, use the TAOR blacklist to fix some issues about AAF spawning too close to NATO.

I hope this helps and if you need more help please comment back and I will try my best. Have fun!

This cleared up a great deal actually, thanks friend!