This is what I have just done:
Make a new multitrack sequence with 8 tracks
Click on the Output Assignments for the 5.1 and use these settings:
Do the same for the stereo track and send it to 7-8
You can now add the audio files to your timeline, 5.1 on Track 1 and Stereo on Track 2
This is the track mixer showing the routeing:
You can now export the file and it will give you an 8 track audio master with the surround on tracks 1-6 and the stereo on 7&8.
Some file formats, like quicktime, will allow you to export audio streams, this will let you have the 5.1 on stream 1 and the stereo on stream 2:
Hope this helps.
... View more