For the life of me I can't figure this out.

Let's say, for example, I want to merge the perks FireEnchanter and FrostEnchanter in the Character->Actor Value->Enchanting. There doesn't seem to be any information here telling these perks what specifically to do, e.g. there's no visible modifier in FireEnchanter that tells it to only improve fire enchantments.

There's probably something obvious I'm missing, but what?

You need to look at the actual perks itself.

Actors > Perk

Yeah, that's what I'm looking at.

Example: FireEnchanter

Modify Enchantment Mod <- double click and hit edit. Perk entry > Enchanment.

Those conditions tells it which element to modify specifically.

Oh! Ha! I never noticed the tabs below "Conditions". To think I've spent so much time pulling my hair out over this.

You're not alone man.

You are not alone.