How you use it depends on how it is wired. If you have all loads connected to the COM terminal, then there is no house and starting battery other than what's on the battery label. If you anchor for long periods without running the engine then whatever battery you want to keep isolated for starting is the one you DO NOT want selected when anchored. In other words, start on BAT 1 and anchor on BAT 2. Under way, select the battery that needs the most attention from the charging system. Remember, charging systems are not an unlimited source of power so to get maximum benefit for a battery, select only the one that is most deeply discharged. If your engine is properly tuned and you know how to start it reliably without repeated cranking, you can start an engine dozens of times without charging the battery.
If you have all house loads on BAT 2 for example, and only the starter on BAT 1, then ALL (or BOTH) would be used for charging at the dock or at home with the on-board charger. At anchor = BAT 2, Starting = BAT 1. You would not anchor with the switch on ALL as you could kill both batteries. So you see, you presented a very vague question that has multiple answers. You are the traffic cop for your charging system and power system. Only you know how its wired and how you boat.