You can leave the jumper on but you still have to do them one at a time. Your best bet is get a 2 bank on board charger. Then you can charge both at the same time without disconnecting anything. You can go fishing and when you get home plug an extension cord in the charger and then forget it until time to go fishing again. If you have a 3rd battery for starting go with a 3 bank charger. Especially if you have an older motor as their charging system is pretty small. It makes life much more simpler.