Water goes into the factory tank, then instead of overflowing back to the lake(your factory vent hole) you divert that to your fatsac intake. Once the fatsac is full, you then run a hose from the vent hole of the sac to the factory vent thru hull to go into the lake.
You could then add an additional pump to drain out the h20 from the sac and out another thru hull, but you can also let it drain back into the factory tank and out through the factory drain. All you need to do is plug the 3rd hole on the sac and as the factory tank drains (from the bottom of the tank obviously), the water from the sac drains into the tank and out that way. A little slower but it works well. I do this on my wakesetter and it works awesome, took maybe 15 minutes, and drains all but a gallon or two out of the sacs. I have them on quick disconnects so if I know I am not using the boat for a week or so I take the sacs out, drain the last couple gallons manually and let the compartment air out a little bit.