Hi fatcat,
the simplest way to do it is to have two Orbiter installations - one for Shuttle launches from LC39A and one for SpaceX operations.
But if you don't have the space on your PC, you could create two new folders in your Config/Earth/Base/ folder, call them "Canaveral Shuttle" and "Canaveral SpaceX". Keep a copy of the default Canaveral.cfg in "Canaveral Shuttle" and a copy of my modified Canaveral.cfg in "Canaveral SpaceX".
When you want to do Shuttle launches, copy-and-paste the one from "Canaveral Shuttle" into the main Config/Earth/Base folder.
Likewise, for SpaceX launches, copy-and-paste the one from "Canaveral SpaceX" into the main Config/Earth/Base folder.
Can't think of a simpler way to do it.
Orbiter does have a facility for loading Surface Bases according to a CONTEXT line in the scenario file, but as far as I know that can only add bases, not remove default ones (so you would have the Shuttle and SpaceX pads on top of each other).
As a side note, I hadn't realised DaveS had not yet released his LC39A pad, so extra big thanks to him for his generosity in donating the concrete hard-stand from his add-on to help me out.
Cheers,
Brian