madiera, that looks like a conventional alternator
which normally has only one charging
output. You don't say, but I am rashly assuming, that this one battery
output from the alternator
goes to an isolation diode "box", a device that has one input and two outputs.
If that is correct, you should be able to simply remove the diode box, connect the alternator's battery
output to the one battery you have, AND also connect the alternator's "voltage sense" lead to the same battery's positive terminal. I don't see a "voltage sense" lead marked on the alternator photograph, but there usually is one. I expect that whatever is being used as the alternator sense lead is being disrupted when you remove the diode box, and that is why the system is (rightfully) complaining.