I have it's the same problem. I looked for help on the Cloudy Nights user forum and I got a solution.
You can connect to the USB port on the handset and then connect the handset to the eq6 unit. Then set the handset to PC direct so it's controlled from the AAP. Set the baud rate to 9600. When I did all that I was able to connect to the mount. I selected EQ mod with sky Safari I think.
I was also told to get an EQ mod cable and connect to that port on the eq6 mount directly from the AAP. I have ordered that cable but it will take a couple of weeks to arrive so I don't know if that will work yet.
Check out the Cloudy Nights user forum. Lots of helpful people there.