The 69 RAIII style lower pan will definately work with a/c. This is the style that has one "ear" of the pan cut off on the passenger side. The 69 RAIV lower pan does not have the "ear" cut off, and is more symmetrical. The 69 RAIV lower pan will not work wih a/c. This was intentional, as RAIV cars were not available with air conditioning.
Remember, the 67/68 pans are totally different than the 69, and nothing will interchange between the pan setups. The 69 uses a small filter up in the hood, the 67/68 uses a traditional baseplate/14" filter/lid.
There are some tricks to mounting that upper pan. Let us know if you need some tips. Not sure if you've done this before.