The glyphs deal damage independently of the staff.
So you will do light attack damage as one value, then if the enchantment isn't on cooldown that will also add the extra damage as a separate value.
Personally I use does magicka damage and recoverers magicka on my resto staff.
I think it's down to personal preference really.
I personally use fire on fire because I am a Dunmer and as it's magical fire damage I went on the assumption I would get my bonus damage from my racial passive.
I don't think elemental weaknesses really pay much of a role within the game, at least not as much as other games. I would say go with what you feel you like, there maybe more optimal set-ups however I am not aware of them.
Couple of notable exceptions... EG for PvP many people use disease as I believe this has a healing de-buff associated with it.