How to go about cooking rock?

So I think its time to cook my rock. Its starting to get undesirable algae and I think phosphates are building. Most of my rock is coral free at this point so I plan on cooking pretty much all my rock. The ones that have coral on them are small (except one that has my giant patch of xenia on it. Is it fine to leave my corals on those and not cook them? It would only be around 5 or so pieces with most being smaller then my fist. The only one that would bigger is my xenia rock which is about a foot and a half long and out 8 inches wide. Its very porous though and doesn't seem that dirty. My other question is how much should I take out? I would like to do it all at once, but I don't want to shock my system either. Any input is appreciated!