OK, I traced out my ballast system this evening. I attached a hand sketch that I made. Let me know if you see anything that I missed.
As you can see from the pdf, my system has a tee plumbed in. The guy I bought the boat from said that he hooked this up to an antifreeze jug, turned the ballast pumps on to fill, and sucked antifreeze into each tank one at a time. This would work but I think that you would need to turn the pumps on to empty after that to be sure the check valves get flushed out.
The procedure ttu posted probably is a better way to do it. Since you fill the tanks first, turn the pumps to empty, then pull the antifreeze thru the pumps and out the drains. This would definitely flush out the check valves in one step.
One thing that seems like ttu's instructions is missing is closing the ball valve on the intake grille. It seems like you want it open at first until you see antifreeze come out of the intake grille. After that, it seems like you would want to close the ball valve in order to force the antifreeze out of the thru hull holes. Otherwise, I think the path of least resistance would be for the antifreeze to flow down and back out the intake grille and never go up and out the thru hull holes.