Audition makes the routing a little wonky, but it is fully supported. You can either run SurCode for Dolby Pro Logic II for an individual file, or in a multitrack session.
File-based Export in Audition:
Pull in a 5.1 source file
Add SurCode for Dolby Pro Logic II as a VST Effect
Tick the grey "Encode" button in the SurCode UI
Click "Apply" in the VST Effect window to encode the LtRt.
(This is where Audition is a little wonky) You'll notice that channels 1&2 contain the LtRt, and channels 3-6 are silent. Simply un-tick (disable) channels 3-6 to the right of each waveform, and use "File>Export>File..." to export a stereo file.
In a Multitrack session:
Create a stereo master-based multitrack session
Add a 5.1 source file to a 5.1 audio track in the session
Add SurCode for Dolby Pro Logic II as a VST Effect. Tick the grey "Encode" button in the SurCode UI.
From here, you can export the stereo master as you would in other session-based work.