Start with the high seam and install one x inch metal to metal screw.
Installing metal roof pipe boot.
Install remaining screws one inch on center around the perimeter of the pipe flashing.
Work up from the initial row starting at the lower corner in a diagonal pattern staggering the shingles to prevent gaps.
A different type of flashing is a chimney pipe boot.
These work better on smaller round chimneys and may be ideal for a stove chimney in a metal roof.
Push your pipe flashing firmly into place.
In this video i cover installing a roof boot for a vent pipe in a metal roof.
Metal roofing is also available in the form of shingles.
The slide the boot down the pipe and leave it about 3 above the roof.
Place the new boot in the hole of the pipe and cut the boot on the line that touches the rim.
Install a second screw on the high seam at the opposite end of your first screw.
Instead of having to cut flashing materials yourself you can buy a fitting boot for your chimney pipe.