I would highly suggest that you run straight up through the roof. They do make flashing specifically for flashing chimneys against corrugated metal roofing. Do a google search on "corrugated roofing flashing for chimney pipe" and there are some good forum threads with ideas. An alternative is to run inside as far up as possible (maintain proper clearance) and then elbow out to the outside, and use a T with cleanout on the bottom to go up above the roof. These methods will minimize the amount of expensive smoke pipe you need. Others will chime in here I'm sure.
Make sure you get the chimney top into clean air, meaning that you are at least 2' higher than anything within a 10' radius. Don't mess around with CO, do the chimney right.
Joe
I have finaly finished a home for my equipment and tractor. I would like to heat it a few times during the winter for maintainence etc. I'm trying to do this for not much $. I have an old wood stove that would work just fine but I've been told that I need insulated pipe all the way through to the outside because of creasolt build. I have black pipe and 1 insulated piece that could go through the side of the building but elbows on the outside are a no no. So I must go straight through the roof. How in the **** can I go through the roof which is corrigated and keep it waterproof so it wont leak? If I use insulated pipe all the way up and go into the side and then up it would be very expensive. Sooo, I could also just use a convection LP heater $130, 40lb tank $89 and be done with it and put the stove on Craigs List. WTF to do?