Can someone tell me what each of the three controls on a 69 heater box does. I have all my cables off my heater control and I need to re-assemble everything.

I think the assembly positions are in the service manual for the 69 as they are for 67 & 68.
It shouldn't be to hard to fiqure out. There will be a door to shut off the heater core supply air for thee upper or function cable and a 'mix' door for the second one and the other probably goes to a vent connection door. This may be incorrect - but you should be able to 'noodle' it trough if you study the cable connection on the control and the door locations on the heater box.

Post back with questions and discriptions of the cable connections and we'll try to fiqure it out with you.