"Plug-in" D2L integration is on my to-do list here as well, as it is also the LMS that we use.
In the meantime, the standard operating procedure goes like this.
A math department admin figure obtains a list of all courses with rosters for each course the weekend before the course starts. This list needs to be formatted a certain way for the WeBWorK server, and depending on how that data comes to you it would probably be nicest to have script do that formatting. Feed this to WBWK, and courses are created with students enrolled.
Actually the courses are created long before that, to give the instructors access. But waiting to the last minute to add students is nice because of all of the flux.
Then the instructors link directly to their WBWK course from within D2L. The instructors also have to manage last-minute additions and deletions to the roster.
Ideally all of this would be linked to your school's enrollment mechanism and happen automatically. This is that item on my to do list for researching.