I would agree, the controller regulates the juice going TO the batteries and not the voltage in the boat, (which is the voltage of the batteries) so your led driver on the lighting circuit would be advisable to regulate the voltage into the led's. Or you can make your own for a lot less than 18 dollars. The solar controller allows you to set the bulk, absorb and float charge levels for your batteries dep on what type and these will always be over 12v (for a 12v system). I'd keep it totally separate from the boat's load system. Although some do have a 12v out connection, I personally would not run all the boat system off that. Aside from if the controller dies so does everything else, the controllers I've seen just don't have a large enough connector to connect the gauge of heavy duty wire that I would expect to see used in anything but a tiny boat system. We have the cockpit LED light wired into the controller, as our controller can be programmed to make the light come on after dusk. There are times when we're producing too much electric, so I fitted a breaker to the electric into the controller, which I can use to shut down the solar power.
Consider http://www.bebi-electronics.com/ for led's they have the controller built in and come with a lifetime guarantee. We're running these for all our lights nav included. You have to rewire your fittings, but I'd recommend these to anyone!
Also consider going shuntless for your battery monitor:
http://www.smartgauge.co.uk/smartgauge.html
"The only disadvantage is if your regulator can display amps used then any power used by the inverter will not be displayed." Another way to view it is to know what is actually left in the batteries for me to use, which is part of the reason I went for smartgauge. Other reasons were that shunt based technology can get out of synch with the batteries and also cause voltage drop.
The smartgauge site also has a wealth of resource material for planning 12v systems. It answered my question "if a bank has more than one battery, connected in parallel, with the load and feed cables coming off the last one, does the first one actually get as much charge/use" One or two people pooh poohed my naive question, but it seems this traditional way of connecting batteries can affect the batteries adversely. http://www.smartgauge.co.uk/batt_con.html
I may be teaching my Grandmother to suck eggs, but don't forget that whatever your total amp hours are on paper, in practise, available amps are ideally roughly only 40% of that, if you want to get as much life as possible out of the batteries. I'd recommend as much battery capacity as you can from the start. But that's just my opinion!
Our alternator (fused) is connected directly to the battery, so is the inverter (its 2.5 KW with it's own isolator switch and fuse). We have a separate 24hr fused system that doesn't run through the battery isolator switch for things we dont want to switch off by mistake - like the bilge pump.
Dont forget also, that fuses should protect the wire and not what's connected to it, and the wires should be big enough to carry the max load and then some, also factoring in voltage drop over the length of wire needed. IMHO I'd over spec your wires coming from batteries to the distribution board and wire up spare breakers and lay extra runs alongside what you need now to allow quick connection at a later date of new stuff.
I may be talking out of turn here, and if you've considered all of this or it doesn't apply to your boat, my apologies. I fear I spent too much time figuring out the rewiring of Crib it became an obsession!
Lesley