Yea it only charges the batter selected. 1 charges 1 and 2 charges 2. 1/2 charges both.

Draining works the same way UNLESS you have things wired directly to your 2 battery.

My sub amp was wired directly to my 2 battery and i kept it swtch on 1 thinking i would be safe. 3 day weekend of rain and spending time in the garage working with the boat stereo on killed battery 2. Battery 1 was at 50% and the switch was on Battery 1

Now i rewired the system and all my stereo is on Battery 2 and only the boat is on Battery 1.

Cruise with 1/2 on to charge them both.

Stop to swim and party, switch on 2 to only run the stereo.

Battery goes dead from stereo jam. Switch to 1 and start boat. Then switch to 1/2 to charge both batteries.

Get home for the night and toss the computer controlled charger on battery 2 for the night.