I have the same flushing set up on my Suzuki 4 stroke. You can flush it without having the motor on. I also remove the pee hole when flushing. I dont know if its the same on a Yamaha. If you flush with the engine on, be sure you have a hoise with the earmuffs attached to the lower unit water intake running. Flushing will not send water to the impeller to cool the engine.
LK