See the attached diagram
In order to separate a single jamLink audio stream to be routed into a single track on your local recording system, you will need to Mute all of the remote and local jamLink channels except for the one that you want to add to the recording. By doing this, only the unMuted remote jamLink stream will be played to the jamLink's Headphone out and into your recording system.
You can still monitor your local playing by splitting the input signal to your local jamLink in front of the jamLink's instrument input and monitoring your local audio through a separate mixer. The local jamLink input signal will still be sent to your remote collaborators, but the local audio (while on Mute), will not be fed back through the jamLink's headphone output, thus isolating the remote jamLink channel that you want to record.
While this is not the most convenient way to record your jamLink tracks onto individual tracks in you local recording system or DAW, we are working on a next generation jamLink that will be much better suited to remote recording with individual track separation and outputs.