If its a GM 3 wire alt. check the following:
1) the main output terminal is connected to the battery - if you have an ampmeter and you are having charging problem - run a wire direct to the battery and see if your problem disappears - this will bypass the ampmeter for testing.
2) the other 12 ga. wire on the 2 connection plug needs to be connected to the main battery cable, unless you have the battery relocated to the trunk. This wire is a sense wire for the internal reg. if the wire run for the main output terminal is long you will get a voltage drop and the sense wire compensates for this by increasing the output voltage.
3) the small 16/18 ga. wire needs to be connected in series with your charging idiot light, the other side of the light gets connected to the run position of the ign. key - its this wire that turns the alt. on/off.
Always use a voltmeter to troubleshoot an alt. installation.