Most good chargers will charge up to three banks, simultaneously.
I'd first verify that your charger
is a multi stage "smart" charger that monitors battery temp and adjusts charging
voltage based on temp, and has multiple charging
profiles for different battery types ,and ideally a programmable profile where you determine voltages.
If it doesn't, then you may want to consider replacing it.
I said may, boats have had "dumb" chargers forever and not sunk, but there is better technology available, if you don't already have it.