I have found the best way to use them is to scatter a few around your home empire to combat religious unrest and then send groups of 3 or 4 out to the holy land. As someone has already said this converts a region very quickly and gives them nice bonuses. You also get some heretics springing up around 80% catholic conversion which gives another +1 piety boost to the lucky one holding the matches. I have also found that having a cathedral or huge cathedral to recruit from boosts your priests much more than a theologians guild. They start off as 4/5/6 piety instantly. A huge cathedral and a theologians guild in the same city is basically a pope factory.

I normally reserve heretics for my upper echelon cardinals to boost them into the preferati or give a high level priest a boost ready to become a cardinal. That instant plus one bonus really helps.