The monitor output goes through an extra amp stage after the DAC so I guess the main stereo outputs are better quality, although I would guess the difference is very small - try a listening test to see if you can hear any difference. The monitor outputs have an advantage in that they are balanced (maybe that's all the extra stage provides?), so should drive longer cables or be more tolerant to interference.
Update: the schematics seem to show both outputs pass through an amp, and they don't appear to be in series as implied by the block diagram, so maybe they are the same after all... or I've just misread the diagram! (see post #4 below)