In the standard CUCV configuration, If your electric fans are 12 volt, they would only be using the front battery. The only time there is power being drawn from the second battery is when a 24V load is applied. In standard configuration the only thing that draws 24v is the starter and the glow plugs when you use the resistor. When the resistor is bypassed, the glow plugs only use the front battery.
A: if your fan is running with only one battery then it is probably 12V
B: if your starter is turning over with any speed at all it is probably 12V
C: due to the glow plug cycle and the high compression of the diesel, even the 12v civi models require two batteries.
If you have electric fans that turn on when the ignition is on, and the glow plugs are on, your starter will probably turn very slow since you drained half the battery before the wait light went out. With the glow plugs getting half the voltage, I am surprised it started. The 6.2 needs hot glow plugs and some rpms to get it to start.
to get real help you need to post some pics of your wiring under the hood. I bet you have a hacked up electrical system and not a standard CUCV system.
the resources are here to fix it yourself and to learn how it really works.
good luck
Rich