The amp gauge is polarity sensitive, and will indicate the relative direction of current flow with relation to the way the wires are connected. The right side of the meter when looked at from the front is the same as the left side of the meter when looked at from the rear. The key is that when the alternator is charging the battery, the meter should show positive, and when it is not (and the battery is discharging) it will show negative.
So, it is very possible for the ammeter to show negative when the alternator is charging, if it is wired backwards. But I don't think that's your problem. Your problem is the alternator is not charging, and the ammeter is indicating the battery is discharging.
A fully charged battery, at rest, should measure around 12.8 volts. When the alternator is charging the same battery, the voltage across it should be around 14 volts. If the head lights are turned on, or off, the ammeter will show the direction of current thru it, and is normally wired to indicate the state of charge towards the battery. The ammeter plays no role in determining the amount of current put out by the alternator (the ammeter is just a gauge or indicator). The regulator enables to the alternator to put more or less current out to match the load including the state of the battery. The regulator on the alternator is a closed feed-back loop, attempting to keep the battery charged, regardless of the load -within the designed parameters.
If the ammeter is wired backwards, it will show plus when discharging, and minus when charging. With the key off, and the lights on, a properly wired ammeter will show discharge, while a reversed wired ammeter will show charge.
You should also note that the headlights are not protected by a fuse. If there were a short to ground, the battery would shove as much current thru the wire as the wire can take (until the heat generated would melt the wire or burn it open). This might cause the voltage to drop, as well as the ammeter to show negative. I doubt you have that issue, but try turning on only the parking lights (which are fused) with the key on and off and see if the ammeter shows plus or minus.