1. Place the new boot in the hole of the pipe, and cut the boot on the line that touches the rim.
2. The slide the boot down the pipe and leave it about 3" above the roof. and begging to caulk around where the boot will go on the roof.
3. Now slide the boot down and make sure there is enough caulk to have a seamless circle all the way around. (never too much caulking so use as much as you want )
4. Start screwing the boot down about every 1 1/2" or so until it is completely filled in.
5. now caulk around where the boot and the pipe meet to make it waterproof.
6. once you have done this look around where the old boot was and look for screw holes and place a nice pile of caulk on each one, then place a screw in each hole. to fill the gap.
7. Now reinstall the Skirt just over top of the boot and caulk the gap around the top.
8. Then Put the top cap back on and if necessary place a screw to hold it on.
9. Clean up and don't fall off the roof, your done
Side note: this is the pretty much the rule of thumb for and pipe on a roof with exceptions to electrical pipes on those you will need a zipper boot. those are a different story. use caution of the roof use boots with good grip.