To create enough cable slack to position the captain’s handlebar you must remove the front brake from the fork so it hangs from the handlebar. Depending on your frame’s cable stop design you may have to loosen the other 3 cables or remove tension from them so the front portion of housing can be slid out of its stop. Remove both handlebars from the stems and set them aside. Remove quick releases, pedals, seats, and seatposts. Unbolt the rear derailleur from the hanger and secure it and the chain to the seatstay with zip ties (in the photos they were put in the parts box because an electronic derailleur and connector-link chain are easier to remove than secure). Place everything but the handlebars in the parts box and put that in the back of the main carton.
Place the wheels in the wheel slot so the rear wheel is in front with the cassette facing left though the big hole. Zip tie the stoker handlebar above the front wheel.
Turn the fork around and place the frame against the left side of the box so the captain’s bottom bracket rests on the foam and the chainstays rest on the parts box. Secure the frame to the holes on the left side with zip ties.
Drop the wheel slot in next to the frame. It will fit snuggly between the cranks and the right side of the case. The cassette should face the frame with plenty of clearance to the downtube and seat tube. If your particular bike results in an uncomfortable amount of clearance fold the wheel slot inside out so the cassette faces the side of the case (we haven’t experienced this but it could be possible given the variations in frame design. It won’t fit quite as well but is better than frame damage). Place the captain’s handlebar in the slots above the front wheel and position it so nothing but bar tape is touching the frame and the box closes. If your particular equipment results in excess contact trim the cardboard to adjust bar placement and/or wrap the portion of top tube.
There’s plenty of space above the parts box for helmets, shoes, etc but keep the total weight under 70lbs for flying.