Hopefully these are simple questions for someone out there.

1.Does AFCAD change/add runways, ILS headings, etc. or does it strictly affect parking? I get conflicting information.

2. How do overlays work? I installed an AFCAD for KSFO, now my sim shows two airports there. I get two ATC voices from the tower. Very annoying. Is this normal? If so, how do I change it back?

3. What help I've found mentions assigning airlines to the different overlays. How do I do this?   

This response is late, hopefully you have resolved your problems/questions by now, but if not:

1. It does all those things and more depending on the ver. of FS and Afcad you have.

2. yes thats normal. (AFCAD2, for some reason dropped the section describing 'overlays'. If you want help with, or an in depth description of  'overlays' you'll need the help files from AFCAD1.4) How to revert depends on where the files were installed.

3. Using 'TrafficTools', a program to add/modify AI flightplans. Essentially you have to re-assign  flights to use the overlay airport.

I know that this response doed not give specific answers to all your questions,  but without details that is difficult. (The overlay section of the AFCAD help file is over 3 pages long, and the method for the removal of scenery is dependant on how/where it was installed, and your ver. of FS)

If you still have questions, posting the name/location of the download, and your FS ver.,  will allow I or others to look at your specific situation and hopefully provide specific answers.  

Cheers,
Dave