Going to drill a 2" hole in the roof (asphalt shingles over plywood) and run a vent for the drains. Help with making sure I have no leaks is what I need. I did roof my own garage so I know what to expect. How to remove shingles to place the pipe flange down and replace shingles?

For Electrical Services(Large pipe), I like to use a 1/4" drillbit maybe 8 or more inches depending on pitch(steeper the pitch the longer the bit.
Then use a hole saw from the bottom, then a hole saw from the top, the long 1/4" bit in hole saw keeps everything in line. Then slip flange under the uphill shingles and Nail and Bull into place. May be other/better methods. Never had 1 leak. We are in a Hurricane Prone Area.

So I am guesing you means you are installing a plumbing vent stack, right? Reach up under the shingles and use a pry bar to carefully pop the roofing nails. Remove 2 rows of shingles and drill your hole, install vent with boot and then reinstall shingles. How to Replace Asphalt Shingles | eHow.com