Secondly, is there away to apply the overlays to helmets added by mods?
Requires a bit of GECK knowledge, but is pretty simple. I made patches that allow the Dragonskin Outfit and Reinforced Chinese Stealth Suit to use Project Nevada overlays and features.
First you need to make whatever armor mod you want to modify a master file (Wrye Flash's "Esmify Self" function, for example) and then just add the helmets to the right Project Nevada form lists (all PN formlists start with PNx, and their names make clear what they do). You can apply vision modes and the stealth field effect the same way. After that, save the patch, load it after both of it's masters (obviously) and remeber to "espify" the armor mod.