Combined batteries with 2 bank charger

Currently I have a dual Bank battery charger for my starting and house battery . I plan to install a switch This weekend to disconnect the power when not in use. The switch is either one on two on or both. The diagrams that I have looked at online Have the Ground On Both batteries connected . My question is that if power is disconnected prior to Charging the batteries independently Would it cause any problems by having the ground side of each battery Connect Or is that just normal procedure .

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I think you are doing a lot of unnecessary work. If this is a newer charger all you have to do is connect 1 bank to each battery and plug the charger in. Unplug it when its time to go fishing then plug it back in as soon as you get back and forget it until time ago again. But if you are trying to do something other than keep the batteries charged I don't know.

I installed a new switch panel that has An LED That stays lit all the time So I was wanting to be able to cut all power from the batteries when not being used. I've always had a dual bank charger So I could charge both batteries independent of each other . But running the batteries through a Disconnect switch I just wondered if it was going to be a problem by having the grounds tied together. My plan is to set the switch to battery one for running the engine And then switch to battery 2 When I am At anchor Especially Fishing at night and using lights.

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It sounds like you are using a battery selector switch. In that case you can leave the grounds connected.

Whichever way you choose to go, I highly recommend the disconnect switches. When my boat is out of the water, the disconnects are turned off. My charger leads go directly to the batteries, no need to disconnect that.
I did this after getting up early one morning, and hearing a noise out in the garage. Upon investigation, I found that the transom up/down switch for the Mercury Tilt/Trim decided to come on and stick in the down position all by itself, and the little 12 volt motor was hot and smokin' as I removed the battery clamps from the posts. New rear tilt/trim switch and new tilt/trim 12 volt motor fixed it, fortunately for under $50.00 thanks to Amazon.
Don't want that no mo, for sure!
Oh, and do a separate switch for each battery, that may help you get back to the house one day!

That's what I want to do, just wasn't sure if having the grounds tied together would effect the charger in any kind if way being that it is a two bank charger. I'm going to run a 4 gauge wire between the negatives and a 4 gauge from each battery positive to each side of the switch. Then the fuse block and positive side of the motor to the common. Terminal. This way I can start the motor from either battery and combine the two if need be with a flip of the switch.

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