Chris, sorry I didn't fully understand the setup you were describing!
However, the "parallel" setting isn't the appropriate one for the scenario you're describing. You would switch to the 2nd battery only. The parallel or both setting would be used for maximum current when starting a cold engine from cold batteries and you needed a large cranking current. In practise, this would be a rare occurence.
We used to have a diesel engined boat with a setup like this and because the batteries weren't very well matched, we only ran one battery at a time, and only charged one at a time.