Charging two batteries simultaneously only works if they are the same brand, same chemistry, same voltage, same amp-hours and same state of charge. Any other combination will result in unequal charging and potential damage to your batteries.
Even if batteries are identical they will still need to be rebalanced occasionally since each has a slightly different internal resistance and charge/discharge behavior. One way to do this is to disconnect everything and then connect them in parallel (+to+ and - to -) for 24 -48 hrs.
As mentioned, starting batteries and deep discharge batteries should never be connected together, either in series or parallel.