Assuming I'm using ancient weapons, and have the barbarian armour set and ancient armour set upgraded twice, which set will I do more damage with with regular attacks, and which with charge attacks (since the barb set boosts those on top of it's attack up bonuses)?
The Ancient Armor Set will enable you to deal more damage, assuming you're using Ancient weapons. The Ancient Armor Set boosts your damage by 80% if you're using ancient weapons. The Barbarian Armor Set boosts your damage by 50% for all weapons.
The Barbarian Armor Set doesn't increase your charge attack damage - it reduces the amount of stamina you use to perform a charge attack. You'll still do more charge attack damage with the Ancient Armor Set, assuming you're using Ancient weapons.