The best I can tell (and it's all still speculation until it goes LIVE) is that in the near future there will be a portal to register your "Commercial" UAS in the same system as the hobby system but a commercial registration will require more information very much like the N# system does. Right now you still use just the "Paper" system within part 47 and part 48.
See below:
The FAA will require persons owning small unmanned aircraft used as other than model aircraft (e.g., for a commercial purpose) to pay a fee of $5 to register each aircraft in accordance with part 48, and a $5 fee every three years for renewal of each aircraft registration. The fees for small unmanned aircraft registration and renewal for this population is the same as that currently required by part 47.