Well it depends. I don't have a schematic for the 2000 Ultra but usually Harley doesn't any small wires connected to the battery. Years ago they did having a single large gauge wire for the general wiring in the bike. But, in recent years, they have moved that wire to the same connection as the positive battery cable connects to the starter. Now, the small wires may be for aftermarket "add ons" that someone has put on the bike like a battery charging pig tail, a security system, or something else. I have no way of knowing. My suggestion would be to get a schematic or try to trace the wires and see where they go. If they are for something like an aftermarket ignition system, which normally connects up at the ignition coil for it's power source, reversing the polarity of the unit could result in damage to the unit.
Good Luck
Steve Bentley
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