The N# registration is what you use for a commercial UAS operation. It's the exact same process (as of this writing anyway) as a General Aviation registration. You fill out a form and mail it in and you get a tail# (N#) assigned to your aircraft. You apply the N# to the aircraft and you're good to go until time to renew.
Hobby registration is registering you as a hobbyist and you use the same # for all of your hobby aircraft. N# is aircraft specific. So if you use 3 different aircraft in your "Business" you would get an N# for each aircraft. It costs around $5 - $10 (depending on if you get a random N# or if you pick one from the ones available).
For complete transparency I only have 1 aircraft that I "currently" use for business so it has an N#. The rest of my aircraft are "hobby" aircraft and when I decide to register I will use the "hobby" portal to register myself and apply the same reg# to all of my non-commercial aircraft. My thoughts are that the N# on my commercial aircraft will suffice for that aircraft whether I am flying it commercially or for hobby so I will not be applying two set of registration #'s on that aircraft. Also all of my aircraft have always carried my full name, phone #, email address and AMA# on them in case of a lost aircraft or aircraft incident.