on a 3 wire gm alternator does the 2 wire connector have to be plugged in for the alternator to charge?

Yes. It can't charge without the field being "excited" by one of the wires in the plug. The other wire goes to your idiot light and it really should be in place as well. Some alternators won't charge without some kind of path to ground on the idiot light wire. Some people use a resistor to ground instead of a bulb.

I have the plug,the small wire goes to the gauge but not sure where the larger red wire goes to.it was charging but I cut 2 wires I thought were dead and now cant figure out where one of them are.one was for me ele. choke on my carb and I'm guesing the other one was for the alternator?
any way the small wire from the connector at the alt. hasnt been touched.on the other hand the red wire has and not sure where it goes.

I lied before, the idiot light is not connected to ground; it is connected to the +12V. That would be the smaller wire in the plug. The bigger wire in the plug needs to go to a switched (as in by the key) power source. Some alternators will let you cheat and connect it to the fat red wire post that runs to the battery. The rest will run your battery down overnight if you do that. You should run it to the key.