I'm not experienced with your interface, and I've messed around a little bit with Cubase SE, so don't take what I have to say as cold hard fact. However, with my Layla/Cool Edit setup, the interface's software was primarily geared towards setting up cue mixes; that is, setting it up so that what was coming in on a pair of inputs could be routed back to the corresponding outputs if desired, for sending to tape returns or spare channels on a mixer. You had to use the actual recording software (Cool Edit in my case) to determine which set of outputs the recorded material played back on, and any given channel could only be routed to one pair of outputs at a time. In other words, say I had four drum tracks: OH left, OH right, kick, snare. If I wanted, I could route each track to its own output (set OH left to output on 1-2, and pan hard left, aka output 1, set OH right to output on 1-2 and pan hard right, aka output 2). This would be most useful if mixing down through a mixer and not in software. Alternatively, I could set each of those four tracks to output on 1-2, and patch that into my headphone amp, and all of the drum tracks would be sent to the headphone amp. If they were all routed to 1-2, I wouldn't be able to simultaneously route them to, say outputs 3-4 connected to my monitors. I would have to pick one or the other.
That said, Cubase seems to have more flexible routing options than Cool Edit, and it may allow you to route a channel to multiple busses, and send each buss to a pair of outputs (ie Buss 1 = headphone amp on outputs 1-2, and Buss 2 = monitors on outputs 3-4). Someone who uses Cubase would have to answer that for you.
I hope that made some sense, but it probably didn't, so I hope I haven't confused you even further. I'll shut up now.
