Agree with skipper724 - seacock in the well beside the sinks/shower gray water pump supplies water to the toilet. In my case, a Jabsco electric. In the 1st pic, that red handled ball valve must be a common supply to the toilet from either the original seacock or the engine room seacock, as you described. In the 2nd pic, the ball valve behind the toilet bowl allows water to the toilet bowl for flushing, and is the same as mine. The last pic looks like the muffler drain? Don't have that on our boat, so no clue. BTW, when moving our boat from Pensacola, after pumpout, to Gulf Shores on the first day of the 16 day passage up to our east Tennessee homeport, we discovered the holding tank was full to the vent. We had left the supply seacock open during this move and guessed the toilet internals were leaking by from the hydraulic pressure of the boat moving through the water, filling the holding tank. We pumped out the holding tank and kept the seacock shut the rest of the trip, unless we were using the head. Problem didn't recur. The red handled ball valve in 1st pic may have been installed for the same reason. With it shut, either or both supply seacocks could left open, and water wouldn't fill the holding tank while underway. Just a guess. I've got more troubleshooting to do on our head to solve that problem.