My Audition only picks up one/first channel on my audio interface

[Moderator moved from The Lounge to Audition CS5.5, CS6 & CC.]

I'm using Adobe Audition cs6. I can only use 1 channel input on my Focusrite Scarlet 212 and my Behringer 404HD. Both have multiple microphone inputs however Adobe only picks up the 1st mic input. I thought it was only the Behringer 404HD then I tried the Scarlet 212 and it still only picked up the first channel. This issue leads me to believe that the issue is a setting in the software that maybe i need to adjust. Any suggestions on what this issue could be?