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No, you are fine doing what you are doing. "All" is used when the engine is running for charging both batteries. If you are at anchor/drifting/electric trolling for long periods of time without running the engine, and you have a relatively high electric load, it is best to isolate the batteries by switching to one or the other. That way you are sure to have a fresh battery for starting in case the battery in use gets drawn too far down.

As mentioned, modern switches are make before break and there is no issue switching between batteries when the engine is running (unless you have a VERY OLD switch.)