I'm looking at the schematics for a 90 YJ and I not sure what wires your talking about. It shows two red and one brown attached to the alternator. There are two red and a green attached to the starter solenoid and there are one red, two green and one black attached to the starter relay. The black wire is the ground wire for the coil in the relay. If you have an automatic, it's grounded through the neutral safety switch. On the manual, it looks like it's wired directly to ground.
If this doesn't answer your question, give me some more info and I'll try again.
jerry
87 XJ 4.0 5spd
90 YJ 4.2 5spd
95 YJ 2.5 5spd