Assuming you are running in 1080i29.97:
Are the clips you are exporting from FCP in exactly 29.97 frames per second (59.94 fields per second)? If you export a clip as 30 frames or 60 fields it will crackle/pop on the XPression output.
You also need to make sure that if you are using the XPression Video Coder that it is transcoding your video files into the correct frame rate as well.
If you are running FCP on a Windows PC you should be able to export directly to the XPression codec.
For controlling audio channels in XPression you can configure the AES channels mapping in the video material.
#XPression