Ok, two batteries (B1, B2) sit next to each other all the time and B3 is some distance away.
*If it was me*:
- I would have B1 and B2 in parallel (as "bank1")and B3 as reserve ("bank2")on a manual switch unless I can figure a way to move them together since running parallel at random distances can be an issue. I'd have a separate voltage level indicator for each bank.
- A charge controller for the pair and one for the reserve (i.e. each bank). Each charge controller connected the same way the bank is connected to the boat (Bank1 B1+ to boat Positive and B2- to boat Negative, Bank2 B3 wired normal.)
- I would put some type of circuit breaker (mainly to act as a switch) between the connector for the solar panels and the charge controllers so I know there won't be a spark with I connect or disconnect them.
- Lastly, If I'm running 2 banks, I would randomly run on the reserve to exercise the battery. Switch to reserve when I know I am coming in for the day.
My biggest concern is having a large and random distance between batteries in parallel. It may work, but it's something I would be nervous about. And if I have the batteries, setting one up as a reserve is a nice safety feature.