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Sorry but not Garris again :-).
The charge is not directed to the battery that needs it per say. What ever battery is connected to the charger is the one that gets the charge until it meet certain specs (do some reading of the links on this site: https://www.bluesea.com/products/7610...4V_DC_120A.
When that battery satisfies those conditions the batteries are connected, just like putting your battery switch on 1+2 or both. Then both batteries are being charged as long as the relay keeps them combined, other conditions might come into play and change what happens. The ACR is nothing but a battery switch that connects the batteries together.

Usual two battery system goes like this, one starting battery and one house (lights, electronics, accessories, etc.) battery. If your starting battery gets discharged trying to start the engine and then it starts, the charge will go to the start battery until it gets somewhat charged before combining them. If you house battery is discharged because you left the lights on all night, then when you start the engine it won't take long for the start battery to met conditions if it was fully charged and then the batteries will be connected and the house battery will be charged by the engine and also drain the start battery, and then they will both be charged. If both batteries are down in charge, the ACR will not combine them until the start battery is somewhat charged before combining them.

Like I said earlier, unless you run your motor for hours with a good charger output and with no other drain your batteries will not be completely charged to 100%. The closer to being fully charged the slower the charging goes. A lot of batteries are never fully charged and do just fine. I'm OCD and want my batteries fully 100% charged when I leave the dock, therefore I keep both of my boats plugged into 120V chargers when not being used.