It sounds like you don't have any fancy charging systems that can look after your batteries for you.
I've been told that if one battery is at say 13.2 volts and the other at 11.9v and you set the switch to "Both" the regulator will sense the higher voltage and will go to float charge mode and the flatter battery will stay flatter.
At present I have a little motor boat with a simple two-batteries-through-a-Perko system. This is what I do and I never have flat batteries:
- Before I start the engine I check my volt meter to see where each battery's voltage is switching alternately to both sides.
- I always start with the switch set to "Both".
- I then set the switch to the flatter battery and let that charge for a dominant portion of the trip we're about to do. That way the regulator senses the lower voltage and charges at a higher rate.
- Near the end of the drive I switch over to the other to top it up as well.
- When on anchor and using domestic stuff, I switch to one battery (could be either one) and don't use the other one at all until the process above starts from the beginning again. That way one battery is always preserved to start the engine and if we run out of electricity on the other (result of "electrical abuse" which doesn't happen often
) then we do without power or we charge up again.
If we're out for a few days, we use kerosene lamps in the evening, an LED anchor light, use the 12v fridge and radios sparingly. I never use the windlass without the engine running. I can't actually remember the last time I had a battery that wouldn't start the engine.
Hope this helps