Follow up to my question: After checking today,my on board charger does indeed have 3 banks. Banks one and two are wired, bank 3 has a jumper wire to bank two. All appears to be factory installed. My single battery is not charging with both battery switches on using the onboard charger (Flybank 20-3). Do all your batteries charge with your on board charger?
Yes they should all charge. If I remember correctly the original charger has an internal fuse for each bank. When mine went out, I didn't even bother. I replaced it with a Promariner Pronautic 1240P.