I've put in a prehung door before but the last one had a brick-mold on the exterior part of the frame and I just pushed it in until it was against the house. The prehung door I have to install now doesn't have a brick-mold, so how far do I put it into the rough opening? Should I just leave 1/2" sticking out on the inside so that the drywall will meet up even with it for trimming?
Keep in mind the exterior finish. Normal is to have some form of frame trim. You can buy brickmold and place around it, attaching to the inside edge of the frame on the outside of the door.
Or whatever siding system you use, has some form of edge treatment. E.g. old milled edge clapboard houses often used simple 1x4s for trim. Vinyl siding has corner pieces and window trim, usually created to allow 3/4" or so of siding to hide under a lip. (Vinyl expands and contracts a lot with temp changes.)
It's generally a lot easier to build up an edge, than to cut it down. Look at various ways this problem is solved, and pick the lowest one.
Approaches: If you have 2x4 prehung door and need to set it into a 2x6 wall, I'd make it flush to the outside, and build up the inside flush with the drywall.