First and most important:
Before even attempting to use the toilet again, pump out the holding tank and rinse it out pretty thoroughly. As Grizz said, make sure the tank vent isn't blocked. You should be able to get the installation/operation instructions for the toilet off the web. Those instructions include drawings showing the plumbing--what's connected to what. If you know the toilet make/model, I can give you the link to the instructions for yours.In a nutshell, your toilet uses sea water to flush it, so there's a 3/4" flush water intake hose from a below waterline thru-hull somewhere to the back of the toilet pump...the seacock on that thru-hull must be open to pull in any flush water. Keep it--and ALL thru-hulls--closed when no one is aboard...thru-hulls left open are the #1 cause of boats sinking in their slips.There's a lever or knob on the pump marked "dry" and either "wet" or "flush"...when the toilet is in the wet mode, pumping brings in flush water and pushes bowl contents out. When it's in the dry mode, pumpig moves bowl contents out but doesn't bring in any flush water. Leave it in the "dry" position except when using the toilet.As for why your bowl is refilling...could be one or more of several reasons: 1. The tank is overflowing and running back into the toilet...2. The run from the toilet to the tank is uphill and you aren't pumping long enough in the dry mode to move the bowl contents all the way to the tank...it's running back down into the bowl...3. It's not backflow, it's flush water rising in the bowl to the waterline because a) you're leaving the toilet in the "wet" mode, and b) the previous owner failed to install a loop in the intake to prevent it. There are a couple of other possibilities, but those are the most likely...and could be any one, two or all three of 'em.The valve in the floor may be the seaock/thru-hull that allows you to flush directly overboard when at sea beyond the "3 mile limit," or it may be a y-valve that goes to a thru-hull somewhere else...I need to know what it looks like to know which. The manual pump in the lazarette has to be the pump that's used to dump the tank at sea. It has nothing to do with the operation of the toilet.That's enough to get you started. I suggest you check out the link below to learn how operate and maintain the system. And I'm always glad to answer questions.