Batteries can kill each other, it happens all the time in golf buggies and trucks as well as 4wds.
When 1 battery craps itself and the other is good, regardless of which it is, if the isolator isnt voltage sensing etc then even though it says on a multi meter that it is pumping 14.5v into the battery, it will be pumping all the amperage into the stuffed one which means the good one only gets surface voltage which will make an older battery die prematurely.
You need a Traxide/Pirahna system and 2 new batteries preferably keeping them the same type and age but with a proper system you can run a deep cycle for a fridge etc and and standard for you main.
Also you shouldnt run your winch off your second battery unless your wiring and isolator can take it, I learned this the expensive way and I had my 2 good auto elec mates pointing and laughing at me as I really should have known that grrrr:(
If you do want to join both batteries (or 2 batteries) to your winch, put in a big mother high amperage switch (one with a big red key) under the bonnet or somewhere so it Isolates the isolator and power runs through the switch contacts instead.
I have seen a Landcruiser which ran 3 batteries all charging off a 12v system and then with the turn of 2 switches (with the same key) 1 to separate (turn off and pull the key) them from the chargine system (and the rest of the accessories) and 1 to join them in series (insert the key and turn on) to run 24v to the winch.
He reconed it worked really well and I cant see any major problems with the system other than you really need to be able to run 3 batteries.
Now I think Ive answered your questions, added a solution and also waffled on about something completely unrelated.....:D
