Bolts or studs and why

I'm sure this is a novice questions but I'm asking it anyway. My Dart has Elderbrock performer aluminum heads. It currently has Hooker super comp 1 3/4 in headers. These headers have to go. I'm not sure what I'm going to do in the final product but in the short term I got a set of 360 high flow intakes that I'm going to use. The question is, when I put the cast iron manifolds on the alunimum heads do I use bolts or do I use studs. Why and what should they be torqued to. Also is there anything I need to be aware of when removing the current bolts out of the head.

Thanks for the help.
Bobby