Position your stove in its final location, at least 18 inches from the wall. Determine the position of your chimney by lowering a plumb-line from the ceiling to the center of the wood stove's flue. Mark this point on your ceiling.
Measure the size of your chimney's support box and cut a square hole of these dimensions in your ceiling, centered around the mark you made previously. Add wood blocking to the sides of the hole and fit the support box into the hole from beneath. Secure it to the walls of the hole with at least three screws on each side.
Use a plumb-line again, this time in your crawlspace or attic, to find the point on the roof that is directly above the center of the support box. Pull up the shingles directly above this point and cut a hole large enough to allow your chimney pipe to fit through it.
Connect the pieces of stovepipe, starting at the stove's flue and stacking upward to the ceiling. The final piece, passing through the support box, will have to be lowered in from above.
Remove the roofing staples on the shingles surrounding the hole in your roof and slide an angled chimney flashing, with a pitch equal to that of your roof, up underneath them until it is centered over the hole. Screw its lower corners to your roof.
Stack lengths of insulated chimney pipe on top of the support box, over the stovepipe, until it passes through the flashing and reaches a minimum of 3 feet above your roof and 2 feet above the highest point within 10 feet. The last few lengths of pipe will have to be lowered from above. Fit a storm collar over the flashing and slide a screened baffle onto the top of the chimney.