How exactly do the armor mods in the title (found in Enemies Within) interact with Pyromancy powers? Do you add the +3 Armour from ceramite armour before or after doubling the armour points from hexagrammic wards?

I would say before, since one is bonus armour, the other doubles the points of armour.

In the end, if you're the Game Master, goes with what is best when running your game. If each time you send pyromancy powers, these are just 1D10+4 fire bolts, then don't go too strong, but if you consider, in all your games, using better fire powers, then go with the all armour *2.

Yeah, I'd count Ceramite first then Hexagrammatic Wards. Hexagrammatic Wards double your armor against Psychic attacks, while Ceramite has already raised your Armor against certain kinds.