The 3 bank chargers have three 2 pair cables (red/black). Each red/black are associated with a different battery.

Just hook up the 3 separate cable pairs to the 3 separate batteries.

The isolation is internal to the unit. Most good units are reverse polarity protected.

Here is the Dual Pro I had with 3 banks. Doesn't matter which output is wired to which battery on this unit. 10 amps is 10 amps.

http://www.dualpro.com/media/pdf/SS3b%20insert.pdf

I always unplug my TM when charging batteries. Habit.