My Honda service manual says to drain the fluid, refill, drive around and then to repeat three times. By my math that makes four total drain cycles. I think the procedure might also be called out in the maintenance section of the owner's manual, but I'm too tired and lazy to run out to the shop to look it up. Honda specifically says NOT to use an ATF flush machine. I have no idea why, but I've done it Honda's way.
Another option would indeed be to just drain and fill 3 quarts every so often, but I have generally chosen to do it by the book. I don't have a great argument for doing it my/Honda's way.