My brothers 90 sammy was having trouble with his alternator charging properly. We tested all of the wiring and the large wire that goes to the battery was fine, but the two smaller wires that plug into the back didnt have any voltage onthem. I looked up the wiring diagram on ACK faq and found that one wire is hooked tot he ignition and the other goes to the dash light. So we tapped into the ignition wire and ran it to the alternator and it is charging bet 12.8-13.8 vlots. Is it ok to leave a one wire connection, or does the other wire serve a charging function other than giong to the dash?

I'm pretty sure the diagram answers that question.

It sounds like you lost your voltage regulator wire.  I would see if you can locate where it connects under the dash then check the resistance, find out of the wire is shorted out or if there is a larger wiring issue at stake.  Do you have 12v on the other connection when the lights are on?

As long as your tied into the ignition on a fused connection you should be ok.  Just make sure it's a relatively unimportant fuse, you don't want a bad connection causing your vehicle to die while driving down the road.