One wire is hot, it would be the ignition wire that wasn't on the regulator. The other two go to the alternator, Field and Earth/ground. I'm just interpreting the diagram posted by Matt.
These wires would be easy to cover with shrink wrap and electrical tape, zip tie it out of the way. Nothing permanent.
These wires would be easy to cover with shrink wrap and electrical tape, zip tie it out of the way. Nothing permanent.