Roof Vents

I have 6 of the plastic square roof vents that are just down from the peak. My question is: if you re-roof, do you install the vents after shingling or is it better to cover the entire base of the vent with shingles. they were just tucked up under 1 or 2 rows of shingles with 1/2 of the flange above the shingles.
any information or opinions will be greatly appreciated.

The flange at the top should be under the shingles and at the bottom should be on top...
Sounds like the roof you are re-doing was done right.

You may want to consider replacing the plastic vents with metal ones as part of the re-roof. The plastic ones have a limited lifetime which will lead to leaks.