I've got an old boat and just upgraded to lithium trolling motor batteries. The trolling motor is a 4-wire plug. When i try to charge both lithium batteries at the same time with a NOCO 3-bank charger, the Voltage light flashes (have each battery to its own bank on the charger) I took a pic of my wiring schematic on the boat for reference. I think the fix is to change out the wiring to the cartoonish-looking pic.

Can anyone guide me so I do it correctly?

If you are not going to use the 12v on the plug I would wire it straight 24v using both red and both black wires together....I always had problems with the 12/24 switch and plug.

Replace the plug. Only connect one set of wires to batteries and plug leaving the other set unconnected or to power something else.

this, you won't want or need the 12v with lithium, wire like the cartoonish pic but eliminate the bottom red/black wires.

With the current wiring setup, should i be able to connect each trolling motor battery to its own bank on the NOCO 3-bank charger and it work appropriately? Trying to diagnose if the charger is malfunctioning.

yes, I have 3 50ah and 1 125ah ionics on a minnkota pc440. I run mine on a timer for 3 hrs. at night since I do have some drain due to electronics.

a manual reset circuit breaker is good, lets you shut all power to the tm while charging.