i don't think you'll flood your engine fueling. the fuel that comes out of your muffler is usually not from passing through the engine but straight from the vent line. i think you'll be fine. as mentioned above, i would count how many cranks when i used a manual pump. i'd count how many seconds when i used an electric pump. but everytime i'd fill her up until i could either see fuel from the muffler or fuel filling the vent line.

good luck!