The answer is in using the Pulse Audio Volume Control to set the capture audio. I use the Jack Connection Kit excusively because my workstation is set up for audio and MIDI editing but you can also set Pulse Audio to send outside of Jack.

I am using 64bit Ubuntu Studio v11.10.

Take a look at my YouTube video for details on how I made these connections.

Look for TheOrganLoft on YouTube.

Good Luck