Can I use my SQ1 Plus as a controller and sound module to use with Cakewalk 9 or Sonar. I have everything hooked up the way i think it should be, but i can only get it to output to one channel. Any help would be appreciated.

The SQ-1 has to be in multi-timbral mode. Not sure what Ensoniq calls it, but on other brands that is called Performance mode (Roland), Combination mode(Korg), Multi, etc...

It could just be that you have to put the SQ-1 in its sequencer mode assign sounds to your different MIDI channels and allow it to receive MIDI data.