To explain the difference between batteries of various capacities (36A, 48A and so on) think of a glass of water. 36A is a smaller glass while 48A is a bigger glass. Think of the car using electricity as someone drinking from the glass with a straw and the alternator charging the batter as liquid being filled in the glass at the same time.
With that said, the alternator has a rated charging capacity, say 40Amp-hour. That means that it can fill our glass at that rate. So the rate at which one can drinking from a bigger glass (48A battery) or smaller glass (36A) is the same and the rate at which the glass is being filled is also the same regardless of glass size, hence it is pointless to fit a bigger battery. Just costs more. 36A battery is sufficient to provide enough power to run all the electrical load if it were all turned on at the same time. And the alternator has enough power to keep filling up the battery with all the electricals on at the same time. If this is not happening in your case, investigation needs to be done as why it is not.