if the manual has the same mods the manual will still win, unless you are talking 10 second cars, or the manual driver keeps missing gears. manaul gearboxes are lighter, you can change faster and at the rpm you want it to change at. if you are talking BIG power cars then an auto can be the way to go.
the best way to launch an auto is, as people have said, left foot on brake, right foot on gas, bring revs up till the car is about to start wheelspinning. if you are coordinated enough you can use the hand brake too. this will add more braking power onto the rear wheels.
using the handbrake is a good way to load up a manual car too. doesn't do the clutch much good though.