I just back from visiting my friend solar energy project. By mistake of battery ordering, he got different battery capacity. It is the same voltage but different the current! With some reason over there, he cannot change them. So, the show must go on he have to use them and the problem is here!!
He connect the battery all together with mixing them up, in the overview it look okay. But some piece of them is not working in the good performance. With some wiring he got two battery different current in series 12V/100AH and 12V/150AH , here the point, the charge controller is working under the average voltage. So, the small current 100AH will be getting the longer charge, it mean overcharge but the bigger current 150AH is never full charge. When the battery is being discharged, the 100 AH battery will go flat ,then its voltage will fall well before the bigger one 150 AH battery. The inverter will eventually cut out but not before the 150 AH battery is excessively drained. So, the small one always work too much, while the bigger is too relax. At the end it will reduce the battery life time, and his solar solar energy is never in the best operation.
Well, I gave him some comment ask them to avoid the series battery wiring with different current. And trying to make the parallel wiring for mixing two battery. Because the battery will be operate under the same voltage, and the current will be shared. But the best is to get every battery in the same capacity/same type. But it is not for his cases.
So, in general you can wiring the battery in parallel , after that the charge controller will take care them.

By Pett Martin : I love solar energy