I estimated the length from the stock battery location to the helm storage area to be about 20 feet, so I went with 1/0 gauge to ensure minimum power loss, particularly since I have a switch in the middle of the run. You may have seen the below chart before.
View attachment 35938
I know it is probably overkill with today's amps that do not draw nearly as much power, but I wanted to be safe. I spent almost $400 on wiring, connectors and fuses, which I think is crazy, but I did it.
My power is fused within 12 inches from the batteries with a 150A ANL fuse. I have 2 amps and the Wetsounds EQ that draw somewhere in the neighborhood of 130A, so I went with the 150A. When I add the 3rd amp for the tower, I will increase the fuse size to 200A.
View attachment 35930
As far as a fuse between the switch and distribution block, it is not necessary. Most of us go with a fused distribution block (as I did) and that is usually overkill since modern amps and EQ's are fused themselves. At that point, you would fuse each distribution leg according to what it is powering. For instance, one of my amps draws 50A, so I fused that run with a 60A fuse. This is insurance but not needed since the amp itself has a 50A fuse sticking out the back.
View attachment 35935
Not sure I understand the Dual Battery question. The batteries hot side (+) should never go to the same bus. The neg (-) can. The batteries will run seperately into the switch and the house side will have just 1 cable going to the helm. At that point, you will only need one positive (+) bus in that area and one negative (-) bus for the grounds. I think you are spot on about the 16A with a 10A fuse into the negative (-) bus for the ACR. I recall that is what the Blue Sea ACR calls for.
I hope this helps.