[Uhehner]

I think you mean you have two cables going to the charger and you have a 12 volt 40 amp three bank charger. One cable should have 3 wires for 120 volt AC from your circuit breaker AC panel, a black (hot), white (neutral) and green (ground). The other cable should have 3 red #8 AWG wires going to each of your batteries, usually via the battery disconnect switches and one black (or yellow) #8 AWG wire going to the battery negative terminal usually via the engine block.
If you do not understand this or have any doubts I suggest you get a marine electrician. An incorrectly connected charger can cause severe engine, propeller, shaft and through hull electrolysis damage.
Capt. george