I've heard that you have to finish Isabellas companion quest in order for her to come back when she leaves later on. I'm basically at the beginning of part 2, except i've done a lot of sidequests, but i haven't talked to the Qunari yet. I'm maxed out friendship with Isabella and in a relationship, but i wasn't able to start her sidequest yet. Does it unlock after i speak with the Qunari, or should i do something else? I'm afraid if i talk to the Qunari leader she might leave afterwards and then i won't have another chance to bring her back. Thanks.

The next step would be to speak to the Qunari.

So i should talk to the Qunari first, and then her quest pops out? I don't want her to leave after i speak. Could you elaborate on that?

There should be a cutscene at Hawke's estate where Aveline and Isabela are arguing before you even talk to the Qunari for that quest.

Yeah, I think you will be directly confronted with the events that lead to the end of her companion quests, like Axxol said.  In any case, you need to be either in a romance with Isabela, or have a high friendship stat, so you should be fine.  Would be better if you didn't know that going in, though. 
 
Also, the first time you meet the Qunari in that Act isn't the moment you're thinking.  You'll talk to them and get some more quests before that event takes place.

You'll have to meet with the Qunari several times throughout Act II. If your friendship is truly maxed, though, you have nothing to worry about.

Ah, thanks a lot. And yeah, i've already boned her ass and got her maxed out.