Test fit the pre-hung door in the door opening. Set the door aside. Lay a level on the sill. If the sill is not level, lift up its low areas by installing wood shims beneath.
Insert a tube of silicone caulk into a caulk gun. Cut off the tip with a utility knife. Run two beads of caulk along the sill, about 1 inch from either edge. Run a wavy bead of caulk down the center of the sill between the first two beads. Run another bead of caulk underneath the pre-hung exterior door's sill.
Set the door's sill into the opening from the outside and push the top up into the opening. Go inside. Insert wood shims between the door frame and the rough opening about 3 inches down from the door's top edge.
Hold a level against one of the door frame's sides. Adjust the wooden shims to hold the door frame plumb in the opening. Insert more wooden shims at the hinge levels, between the frame and the rough opening along both sides.
Back out one middle screw from each of the door's hinges and set aside. Replace these with 3-inch wood screws driven through the door frame, wood shim and into the rough opening.
Open and close the door to check that it works smoothly and doesn't rub against the door frame. Hammer casing nails through the door frame and into the rough opening every 16 inches, along the door's knob-side jamb and header jamb.
Return inside. Score along the wooden shims with a utility knife. Bend the shims back and forth to break them flush with the door frame. Spray expanding foam into any visible gap between the door frame and the rough opening.