I don't know anything about how your batteries are wired except from reading the above posts, but if one isn't already installed, there's a thing called a battery combiner that I think would help in your situation. I installed one on a bigger boat I used to have and it worked flawlessly and my aux bank was always ready to go, and with no danger of me forgetting to deselect them and running down my starting battery. I realize that an aux bank isn't the top priority, but it's really bad for any battery to sit in a low charge state, so I think it's important to do everything you can to make sure they can easily get charged and stay that way until needed.
A battery combiner is an electronic device that closes the circuit between batteries when a certain preset voltage is present, but then opens it when the voltage falls below that level. So, for example, you could choose to set it at 13 volts and any time (during charging) your starting bank reached that level, you would also be charging your aux batteries. When you turn off the motor, they would stay combined until your voltage fell below 13 volts and then the circuit would open, ensuring you'll always have plenty of juice in your starting batteries to get your engines running again. There is also an override switch that allows you to close that circuit manually in the event you need your aux batteries to help start your engine. I think I paid a little over $100 for the one I bought about 5 years ago and it was easy to install myself.