Everyone has always told me that the batteries should be the same age. However, I think you have another issue because they are some distance apart. I think I would consider another switch and charge them separately and run them separately as well.
I don't know why you are needing the second battery, but if you haven't switched to LEDs, you probably should.
Finally, I'd measure the compartment and potential batteries. All Group 24, 27s, etc aren't exactly the same size and they also are different amp rated as well.