i have used black for both positive and negative all the time i simply crimp a red insulated connector to the pos and a black insulated connector for the neg. That way there is no confusion when changing out a battery, hooking up something else, etc. The installer should have identified the wire as being positive either by red tape, a rep insulated crimp connector, or so on. I would not rewire anything, however.

If you get into factory installed systems, you will find blue hot wires, brown hot wires, wires with stripes, black hot wires, and some very mystic color coding schemes.