Inquisition? As I expected . . .
As to OP's question:
There are, as I understand it, 5 distinct layers for armor, not counting implants or natural armor. All of them can hold modifications like elemental prots or stealth helpers:
Second Skin
Form Fitting Body Armor
Armor (i.e. full armor suits, riot gear, armored clothing, etc. This is where most of the armor falls)
Securetech PPP systems
Coat (greatcoat, lined coat, etc,)
For mods, I'd suggest covering the damage your mostly likely to run into (electric and fire are usually at the top). Don't forget gel packs!
Helmets can be handy, especially if you're wearing a full armor suit and can incorporate a RIG system and a chemical seal. They're not mandatory though, as most of the other functionality can be put into eyeware and your commlink.