First things first.
1. Take a voltage reading at the battery terminals with the engine off and write it down.
2. Start the engine and rev it up a bit. Write down that voltage.
If the second voltage reading (running) is less than about 13.5VDC and you're sure your battery
is okay, proceed. If, on the other hand, your non-running voltage is below about 12 and your
running voltage is at 13.5 or above, you have a battery problem.
I mentioned the dual battery system and the isolator.
If, like me, you opt for an isolator rather than a relay in your "split charge" system,
and your isolator is not one of the more efficient ones now on the market, you are losing
some charging voltage through the isolator. Though your charging system would otherwise
be adequate in the stock (one battery) system, it may need a little help from you to compensate
for the loss and get you back to keeping your batteries in the best state of charge.