With most Pioneer hardware you will first need to go into Pioneer's setup utility and assign a stereo pair of channels to be the "MIX (REC)" channels. Next, if you're recording in MixEmergency, select your Pioneer hardware as the Device, and make sure that you set the channels to the same stereo pair as you assigned in Pioneer's setup utility. I don't think that there is an option to select audio channels in Syphon Recorder, unfortunately. I haven't used it for some time though, so the app may have gained this feature.
