Fred-
The two batteries in the starboard lazarette must be a tight fit! Are they group 27's? Too bad they're both on the same side and also on the side of the helmsman-very unbalanced when out alone!
Some of the newer boats have room between the gas tanks for two batteries amidships on the floor. If I had room in my older '87 Cruiser with the original Moller tanks, that's where I'd put 'em both (lowers center of gravity). Currently I have one in the starboard lazarette and one between the tanks, which seems ok, especially with the water tank under the rear dinette seat full and some minor weight shifting.
If you don't use your port lazarette / bait well for bait or as a live well, I'd still preserve it's intended usefulness as a live/bait well by routing the cables through the drain and or water inlet. Should you sell the boat to move up to a 25 or for unforseen reasons, it will be more salable that way. You'll probably have to use both to get 2 gauge cables to the battery.
Does your lazarette lid leak? If it does, be sure to put the battery into a covered battery box. You may also want to seal the cables with silicone at the drain and inlet, but then how does the water get out? Maybe just seal the lid as tight as possible and just let any leak water drain into the bilge to be pumped out by the pump?
Run the cables either at the front or the back, just a long as 1)access to them is as easy as possible, 2)they look good (hidden), and 3)they're up and dry of the bilge. 4) Most Important: Keep them away from friction contact with the tank and fuel hose components. A unlimited amperage short on top of a gas tank and you WILL be buying a new boat!
A big fuse or circuit breaker would be a good idea on any installation that has a reasonable chance of shorting out. Usually battery-to-battery switch and switch-to-motor connections do not have these to eliminate any extra resistance in the circuit which would drop battery voltage to the starting motor, which then leads to high amperage draws / overheating /shortened starter life.
If you can keep the cables up out of the way and held with rubber grommeted fasteners and grommeted through the drain and inlet, etc., you should be ok w/o the interruptors. The cables could also be sheathed together with a split cable wrap over problem areas. Wrapping them together with electrical tape would be ok in freshwater applications, but I wouldn't want to have a set up where salt is held inside of anything, even with the plastic covers over the wire inside. A more expensive solution would be to use duplex cable, which has two cables wrapped together with a material and then a plastic outer cover, but it's very hard to find in gauge 2 and probably costs about $10 a foot (6 gauge is $5.29/ft @ WM).
Be sure to use tinned marine grade battery cable back there. Salt water migrates up any exposed cable or wire and is not completely washed out with the daily rinse down, and salt corrosion then destroys the copper strands. Also use marine grade tinned lugs on the cable. Don't try to cheat and use smaller diameter cable because of the voltage drop problem. The extra cost is much less than that of a new starter.
Sorry if I've over-explained this, but I'm a retired H.S. teacher and have developed a habit of trying to write things so that others who read things later without the background of our more experienced members can learn as much as possible by making all the connections. Joe.