You have a potentially serious problem
Obviously, your head is below the waterline...leaving the head in the "flush" position allowed water outside the boat to try to seek it's own level inside the boat....it's a good thing you were aboard when the head flooded, or your boat could have sunk! Although the head seacocks--in fact, all seacocks--should always be kept closed except when the head (or whatever is connected to the seacock) is actually in use, because human beings are fallible, it's never a good idea to rely solely on such things as remembering to close a seacock or leave a valve that can also fail in the "right" position to protect your boat. To be sure it doesn't happen again, you need to install a vented loop in the head intake line--between the pump and the bowl, not between the thru-hull and the pump--that's at least a foot above the waterline at any angle of heel. It's a 9 year old boat...if you don't know the age of the toilet, or how long ago--if ever--it was rebuilt (all the seals, valves and gaskets replaced), do it...or if you can replace the entire head for about the cost of two rebuild kits, just replace it. As for your shower, I suspect it drains into a sump...so you need to find the switch for the sump pump. And as for whether pumping out actually succeeds in emptying your tank, never assume anything...check the gauge to see what it reads...if you don't have a gauge, visually inspect the tank. To learn more about your system and how it's supposed to work and be maintained, I suggest you take the time to read the articles in the reference library in the Head Mistress forum. They're a fairly complete "boat plumbing 101" course.
