The manual and the tutorial's demonstrator speaks of having each output have it's own EQ, Dynamic, etc.
That is correct, and this is possible.
You may be confusing what the manual means by outputs. The outputs the manual is referring to are the
physical outputs on the back of the MOTU unit. Each stereo pair can have it's own effects of compressor, EQ, or Reverb.
Watch this video. It may help you:
http://www.youtube.com/watch?v=48vYfBl3DaU You can also apply the effects of CueMix FX to tracks in SONAR by using the Return Assign.
For instance, say you apply some comperssor on the outputs Analog 3-4 and you want to record that on a track in SONAR. In the MOTU Audio Console, you select Analog 3-4 as the Return Assign, and in SONAR you create a track and for that track's input you select "Stereo MOTU Audio ASIO Return 1" as the tracks input, arm the track and hit record. That will record whatever effect you put on Analog 3-4 output.
And for Reverb effects applied by using CueMix Reverb, see the video I gave a link for, and to record the Reverb to tracks in SONAR, as in the example above, select "Stereo MOTU Audio ASIO Reverb 1" (instead of Return 1), as the input for a new track.
See page 32 of the MOTU manual, and read the CueMix FX section of the MOTU manual, page 63. That may help you better understand.