In this case the batteries absorb from the alternators the same amount they give to the on board plants. The automatic battery charger employ the same criteria. First it will provide the energy required to re-charge the batteries, and then it will deliver the energy required by the on board plants. Some battery charges have a manual option which allow to keep on charging the batteries even after they have reached their maximum capacity. This operation is, however, extremely dangerous, because it cause batteries overheating which can seriously damage the batteries themselves.
Every alternator is connected to a batteries set.
It is very important because, when you start the engines, you have to start first the one which is connected to the engines' batteries, so that the other engine will surely start. Before you start the engine you have to disconnect the battery charger so to avoid interference with the alternator . This is a good practical rule although most boats are fitted with circuits especially designed to prevent this problem. The generator set has its own starting battery, which is charged by the generator itself. Check, when you buy them, that they are long enough to reach one of the batteries on board.