Well when i fight rebels i allways have priorities :
Attack Religious rebels before they start spreading their faith(first priority)
Attack Patriot rebels before they become part of another country(second priority)
Attack Nationalist when there are no need to deal with those two other rebel types, if you can, asap, however it is not a tragedy if they win, as you will be able to reconquest them for 0 infamy.(third priority)
Attack Peasant rebel before they will give you nasty flag of -50% tax(fourth on priority list)
Attack heretics after peasants as they also give nasty flag. But peasants will die after one battle, so you will deal with them faster, and you will be able to kill them easier(fifth on priority list)
Other rebel types except pretenders, must be dealt after those.
Pretender rebels can be dealt in the end, as they are strongest, and you don't get bad flags. Sometimes they even give you a positive, by taking over, and giving nice ruler. Plus to kill them, you only need to kill ONE rebel stack of theirs, and then all pretenders in the kingdom will die, and all provinces they taken will be yours again.