I am not 100% familiar with that receiver (last used it over a year ago) but I don't think it supports ppm. But I could be wrong as there is a v2 now.
As for only throttle working, have you run the radio calibration process when setting up your APM 2.6? Ifbits all connected properly you should see it all working. Otherwise it could be a setting issue on the turnigy 9x. This video should help you get it all setup.