Your practice is okay for day sailing, but can get you in trouble when cruising and away from shore power. With the batteries switched to "both", if they ever got too low to start the engine, you will have a problem. So for cruising, you should use one bank or the other except when under power, in which case you should switch back to "both".
I got nervous about the possibility of forgetting to switch batteries while cruising that I changed the power wiring completely to have dedicated start and house banks, and a battery switch that is either "on" or "off" except in emergencies. I
did that before Spring launch and have really appreciated it. When I'm using the boat, the switch is "on", and it's "off" when I'm off. It did involve installation of a new charger (which I needed to do anyway) and running a new alternator output cable. With the addition of a flexible solar panel on my dodger, I rarely connect to shore power, which is an added bonus.