The corroded breaker in the first pictures is 25 amp. I would replace that. Then do the following. What you need is a 12volt test light with a 20ft jumper wire. You can make a jumper wire with a 20ft piece of wire and two crimp on alligator clips. Clip that to your test light and the NEGATiVE pole on your battery. Make sure your big red battery switch is on. Then trace and test all connections going to your head. For example. Test for power at the button/switch.
I would suggest that you disconnect the battery grounds (to avoid shorts) and then unmount the battery switches. I can't say if you need to disconnect the wires at the switches yet, it depends on how much slack you have. Now you need to take pictures of everything especially the backs of the battery switches. Make a drawing of every wire and connection including any and all connections at the batteries. If you remove any connections, mark the cable with a piece of tape and documenting where it came from. Now you need to trace as well as possible, where the cables go.
Regarding the breaker for the toilet; At the moment that is the least of my concerns. It is obviously incorrectly wired. I can't tell you what to connect it to yet since I don't understand the wiring right now.
One more time, I will list what there should be normally.
Some loads get connected to unswitched battery voltage. In your case, that is probably just the automatic bilge pump feeds. If you have two bilge pumps and two or more batteries, generally each bilge pump feed connects to a different battery ( so that one can still work if the other battery runs down).
If you have a battery charger, the outputs would connect directly to the battery and should be fused near the battery))
Some stereo radios have a memory feed that is also directly connected to a battery to keep your pre set channels memory. That should also e fused near the battery
If you have two or more batteries and two switches, note that each switch has two inputs, usually battery one and battery two and one output. In addition for dual batteries, there will be heavy gauge jumpers that connect the two switches together so that each switch can select either battery (or both)
This is important to remember: A direct connection to a battery can be made at the battery terminal itself OR at the input terminal of a battery switch(since that terminal is directly wired to the battery). That is why you have to undo the battery switches to see what is on the back (assuming rear connections which are most common).
The main boat feed for all accessories comes from one of the switches output terminal. (In other words, the accessory feed will not be live unless the battery switch is on). That wire will be a lot smaller gauge than a battery cable but will still be larger that most wires used for accessories. That feed has to have over current protection near the battery! The capacity of the breaker can not be greater than the allowed current in the feed based on wire gauge and total run length ( that includes the length of the feed AND the length of the ground return.
It is also very important to note that you can't size the breaker for more current than the ground wire is sized ( weakest link theory).
OK, so let's say in a typical application, we now have power wired via a battery switch and a breaker to the main DC bus or panel. Usually all accessories would be connected to a fuse or breaker at that panel/bus. Some loads perhaps like your toilet, may be connected to the 12v bus directly and not through a fuse, in effect an extension of the accessory bus.In that case there must be a fuse or breaker somewhere before the load. In your boat, it seems that a breaker was mounted at the wall behind the cabin. That's OK as long as wherever that breaker is getting power form is also protected as described above.
Although it doesn't seem to be the case on you vessel, many times accessories are added that require more current than the accessory bus was designed to carry. Windlasses are the more common add-on that can run into this issue.
In those cases, it is often necessary to run new feeds both ground and positive directly to the battery switch and battery ground. In that case just like the regular accessory case, over current protection is required at the battery area. Yes, windlasses usually have a breaker at the dash but that in itself does not meet the requirement for over current protection. ( as a side note, the breaker at the battery should be sized larger than the one supplies with the windlass so that should the windlass pop a breaker, it pops the one at the helm and not in the battery compartment..
Remember the goal is to make sure that wires don't overheat and catch fire due to too much current draw or a short.
If you don't feel comfortable with wiring and are not familiar with the theories and best practices, you should get help
I would'n normally be typing such a long message but I am getting really bored staying home. In addition the weather lately hasn't been all that great and is depressing.
Have fun!