It sounds like you're hooked up right, so there's no reason the ammeter shouldn't deflect in both directions if it's OK internally. Is this an original-equipment ammeter, or an aftermarket item? Try this- - - - -connect a battery charger to the battery wire at the regulator with the engine off, and see if the ammeter shows a deflection in the "charge" direction. The battery charger gtound can attach anywhere, either at the battery, or any point on the engine block, etc.
Is the battery staying charged, or have you run it long enough to tell? Voltage at the battery terminals with the engine running should be above 13 volts if the charge current is getting there.
Jerry