Either way your talking about will work fine just take twice as long to charge. I have a 10 amp , 3 bank. Onboard charger....MinnKota 330D. One bank connected to outboard cranking battery and the other two banks connected individually to the trolling motor batterys....yes the jumper stays in place. When i come in from fishing I plug it in......it stays plugged in 24/7 untill i go again.