There are two ways in which you can take audio into Compressor and ensure the correct 6 channel configuration in the DCP you are creating.
1) The first option is to export a video-only QuickTime file and 6 separate mono sound files from FCP (or which-ever editing system you are using to edit). Then use the “Add Surround Sound” option in Compressor to map each file to its respective channel and attach the video-only QT file to it using the “Add Video” button in the same window. Please see screen-shot attached named “Surround Sound”.
2) The second option is to create a Video-only QuickTime file and a QuickTime audio file with the correct 5.1 channel mix from sound-track pro (or any other audio mixing/editing software since this option is not available in FCP). The 5.1 channel mix is DIFFERENT from a 6 channel file, screen-shots of the correct and wrong versions (labelled as such). The “6 channel” version will not work in Xport.
Then attach the video-only “mov” to the “audio-only” mov in Compressor.