Run the hole saw w/long bit up from the bottom, don't try to drill all the way, just enough to get the long bit through the roof. Now go up on the roof and carefully cut out the shingles the approx. size of the hole saw. Now take the hole saw/bit and place the bit in the hole. That will keep you at the same angle that is was from beneath.
Hold the drill firm and start drilling slow until it gets a good start, then finish the hole. It will be, if done right, a close fit. Even if it's off a little the boot will cover it.
Plan "B" is to use an old worn hole saw on the roof without cutting the shingles first. That way you won't ruin a new saw.
Better plan is to borrow the plumbers hole saw!:angel: