cut a hole in the bed straight up from the exhaust.
take the stack, and put the adapter on it to go from the size of the stack to the size of your exhaust.
then put the stack in the hole, with the top of the stack where you want it in relation to the top of the cab, that will tell you if you need a short piece of pipe to get the 90* elbow lower and inline with the rest of the exhaust.
when its in line, put a piece of flex pipe between the 90 and the rest of the exhaust.
then cut the exhaust so it fits inside the flex pipe, and remove the rest from the truck, as you will not be using it anymore, as you now have a stack.
keep in mind there is a cross member there, right where the stack needs to go if you want it as far forward as it can get in the front of the box. you will need to notch the cross member out approx 1-2", otherwise the stack will be that far back from the front of the box. its a preference thing. i notched mine, my buddy did not. no difference in ours, except his has a 2" gap between the stack and the top/front bed rail, under the rear window.
if you talk to paul at complete performance there is a "stack bracket" that mounts to the floor of the bed, that makes a real clean look where it comes through the floor. you will also need some sort of a clamp to hole the stack to the bed rail, or where ever you decide to support it.
ill see if i can get paul to comment in here with some pics i know he has.