Wiring harness
Agreed. The PATS system should not be related to a proper stereo installation.
Pull the radio, and make sure that the previous installer used an aftermarket harness. The aftermarket harness should plug into the factory harness. Then the wiring connections are all downstream from the factory harness. These aftermarket harnesses are inexpensive, and come with instructions and a 800 number for questions. The only difficult item to aftermarket harnesses is that each aftermarket harness unit covers many vehicle models, such that the wiring codes and colors are slightly odd, and there may be colors and codes that connect without matching perfectly. Remember, these aftermarket harnesses are not expensive (translate "cheap"). The toll free lines are a good resource.
But the most difficult situation you could have, in my opinion, is if the previous installer "saved" the money fot the aftermarket harness, and clipped out the factory harness connection. This would leave the radio wiring going directly to the guts of the vehicle wiring with no harness connection. This situation could get nasty, and I might pay a professional installer to resolve that.
In either case, you will be able to get this resolved.
Good luck with the installation.