No - they can be different amp hours without a problem, batteries have an 'internal resistance'. As they get changer the voltage rises. If one is flatter than the other the flat one will have a lower voltage compaired to the output of the charging system and hence more current will flow to the flatter battery.
Connecting two batteries together just creates one bigger battery, with a combined amp hour.
What sort of split charger to you have ? an electronic one or a diode one.
Either way if you connect a battery before the split charger this will pull the voltage down /up going to the split charger. Causing it not to function as well as it would, as the alternators regulator will get confused as well
Best option is to have the two leiser batteries in one bank for aux circuits, and the starter motor batter on the other bank doing the starter motor and main circuits etc.