Currently Being ModeratedApr 18, 2013 2:45 PM (in response to Adam Berch)
Both self-contained or reference will give you the same quality.
I use self-contained most of the time as Compressor seems happier with them and I have lots of space on hard drives.
Currently Being ModeratedApr 18, 2013 3:23 PM (in response to Studio X)
Export self contained. While both are lossless, the reference file is smaller because it references the media in your capture scratch and render files. Move it to another computer, or if any of those file go missing, that file is useless.