I didn't read carefully enough.
You have a duo charge controller so that is like having 2 separate charge controllers from one panel. I wired a small single
Mornigstar controller yesterday so the duo is probably similar. ( that one was to keep a car charged while I'm away)
There will be 2 terminals probably on the left showing + and - for the panel. If you are not sure use a cheap
digital multimeter and it will show something like 19v with the panel in the sun and if it is -19v it's the other way around.
Then to the next right there should be 2 sets of terminals with a battery
symbol on each maybe labeled bat 1 and bat 2. The + and - of each goes to each battery and they will be isolated from one another in the controller. Always put a fuse (spade is best) near the battery + terminal connection of each.
Then next right with Morningstar there is probably a + and - terminal with a light bulb symbol for an auxiliary connection. I usually ignore them but make sure the screws are tight. Then there should be on the far right side 2 terminals with a small plate connecting them. If you have sealed batteries leave the plate in and then the max charge will be limited for sealed batteries that you can't top up. If you have flooded batteries that you can top up with water
take that plate out and throw it away.
As you want to be able to isolate each battery from one another put a heavy starter type cable from each battery + to each side of a decent isolation switch. The 2 negatives are joined together at whatever common earth you have, probably your engine transmission
connecting bolts. Don't have 2 battery earth connections in 2 different places on your engine as there could be a slight voltage difference between them which could increase electrolysis
You should of course have another isolation switch on each battery + going to their respective loads i.e. starter or house etc.
The fuse size on the controller battery + connections depends on the panel size but would normally be 5 / 10 amps. If you are not sure try 5 amps and assuming your wiring
is OK if it blows go to 10 amps.
The controller should be as close as practical to the batteries. That is to avoid regulated voltage loss in the connecting cables
. The length of the panel cables
doesn't matter as much as the voltage in them is unregulated.
All your wiring
should use tinned marine
cable including the battery cables as plain copper rots away in salt
I have 3 Morningstar controllers but not a dual one. I'm just going by their usual layout of terminal connection.
I see you are in Monterey. We enjoyed a couple of days there last Oct and looked around the yacht marina and at the resident sea lions, and had fish
and chips on the pier as you do. I don't envy your fogs and I suppose you can sail out past them.
An Alan Wright design will be a good sound cruising boat. I once had the pleasure of meeting him in his very small design office overlooking the Hauraki Gulf in Auckland
NZ about 20 miles from where I live.