[Juzza]

1.way to use them is if you yourself have a weak dominion to lower enemy dominion in your own lands.

2. if you have, lets say a -3 drain dominion but you want to be able to research alright, well just chuck a few heretics in a province (not too close to your capital, god, or prophet) and research away in a nice 0 magic environment. This should be combined with a strong dominion.

3.Ever been in one of those really important sieges? where it's your god, your prophet and your biggest army, vs there god in there capital, and no matter what you do you can't get their dominion down? Heretics are the answer!! combined with your own priests you can drop an enemy dominion in no time!

Thats just some uses, theres probably more out there, personally I don't use them that often, except for the research one, thats a handy little trick.