Or do you mean the ammeter is showing charge because the fans are hooked to the battery?

Like shown here: http://www.heritech.org/cuda/Charge2.html#Problems

If you're OK with the fans running only when the engine is running,have the relays pull the power from the alternator. Then the ammeter will only show what is going to and from the battery. Plus, the fans will be getting power right from the source, instead of going the long way around and through extra connections.