I was recently doing a delivery from Newport RI to Norfolk VA with the owners of a Caliber 40. The owners had been living aboard since they purchased the boat three years earlier, but had not done much sailing. They hired me because I am an experienced/licensed captain and a sailing instructor.
The autopilot aboard stopped working as soon we set out, and for the first three days. The owner thought that the fluxgate compass mounted in the bilge below the pullman berth was the heading sensor used by the autopilot, and for three days he was rearranging the tools and other crap that he had stored nearby. On the fourth day I was in the lazerette, resolving another (fuel) issue, when I noticed another fluxgate compass mounted high on the bulkhead between the lazerette and the navigation station. I had placed my laptop with a BU-353 (USB) GPS receiver in the nav. station on the other side of this bulkhead when I came aboard. My BU-353 GPS had a magnetic mount. I quickly figured that THIS was the fluxgate compass for the autopilot, and moved the GPS receiver away. We never figured out what that other fluxgate compass was for.
My point is that you should DOCUMENT where all of the components of your autopilot installation are mounted so that if you ever sell the boat, or put it into charter, or hire a captain to deliver the boat for you, that the skipper can have a fighting chance of troubleshooting problems with the electronics.