The first thing is to make sure that pr-hung doors fit the openings, if not you may have to make some adjustment to the openings. Next make sure the house wrap is stapled in place around the rough framing as you did with the vinyl windows.
Before the pr-hung doors are set in place ,three (3) beads of a good quality exterior caulking are placed on the floor where the threshold will rest. This is to seal the threshold to the floor. Another bead around the edge of the opening will seal the sides.
Now put the unit in place by placing the threshold into the caulking first and then pushing the sides and top tight into the wall. With someone on the inside check whether the unit is centered in the opening,if not make the necessary adjustment.
From the inside make sure the door is centered in the rough opening. With a level check the hinge side of the frame and make it plumb. At each hinge, shim the gap between the rough framing and the door framing. This will ensure that the frame stays plum when fastened in place.