I want to alter the intense flames perk so that it is actually useful. Fear, in my opinion, is rather useless. So, I figured why not alter intense flames so that it deals double the burning damage? I looked up on UESP that burning deals about 10% of a spell's damage dealt. How do I alter the burning damage? Do I have to write a custom script?

I don't know if a perk can alter damage directly.
And I cant find out for you, since I dont have access to a CK right now.

However, I do know another method.
You can add an extra effect to all flame-spells, that only enables when you have the Intense-Flames perk.

A good example for this would be the enchantment on bound weapons. It has multiple effects, but the soultrap-effect (for example) only enables when you have the correct perk.