It has an extra sub out, that is the same as the Preout sub channel, it is just a benefit for those that want to run dual subs and not have to use a Y splitter, but either way will work just fine Y or straight out of the second sub out...
They are the same signal, not separate (stereo L & R) so your choice how you want to hook it up. If your using the Y splitter you may have to boost the sub out channel a few db's, no big deal. I'm not sure if you would have to bump up the sub db's if you use the second jack or not, only testing will tell with a meter when level matching sub level to the mains, or if others can chime in on this. Depends on if they linked both sub outs together internally or not.