In response to markdelorenzo's question, you can definitely have the Atom connected to one track and the Atom SQ connected to another. By default, each track's Instrument Input is set to All Inputs, and when that particular track is armed to record, you can use any connected controller. However, you can assign specific controllers to each track if you desire. With your track selected, click the "i" (Inspector) button at the top of the track column to open up the Inspector column, then go about halfway down and you will see Out/In/Channel. To the right of In is the Instrument Input dropdown menu. Click on that and select the controller you wish to use with that track, repeat as necessary. You can also find the Instrument Input dropdown directly below the Instrument Output in the track column, but, it is hidden by default. To make it visible, you need to expand the height of the track by setting the arrange view Track Size to Medium or Larger, or by clicking on the bottom of the track (in the track column) and dragging down to expand it vertically.