Ie: If I have the augmented flames perks, will a bow enchanted to do fire damage do more damage?

Yes. For example, if you have the first level of augment, your firey soul trap bow will do 12 fire damage instead of 10. At the second level 15 instead of 10.

The ultimate is having 100 enchant and the dual perk. Then the augments of each part work in the other part so you can get around 69 damage for each effect.

Awhsum!