I have two batteries in my boat that are wired through a barrel switch. The switch enables me to switch from posit 1,2,both or off.
I run the motor and electronics off the main battery and both downriggers off the deep cycle marine battery.
My reasoning is that if somehow I run down the battery with the downriggers, I am still able to start the boat since it's running on the other battery.
With the barrel switch in posit 2, they both charge up heading out and coming back in.