Alesis IO4 USB Interface routing question

[2BFrank]

Hi,

I have an Alesis IO4 USB Interface that works great with my KXStudio 12.04.

However, I have one thing that I haven't worked out yet: When recording 2 tracks (Inputs 1 and 2 on the Alesis) at the same time with Qtractor or Audacity (via Jack),
they go to one single stereo track instead of two separate mono tracks.

What do I have to do to route each signal to a separate track? Is it a setting on the Alesis or in the software?
Thanks for your help!!