How can our league set up a rookie draft?

Fleaflicker has full support for multiple drafts per season, including rookie drafts.

If your league has already drafted, add a supplemental draft: League >> Settings >> Add a Supplemental Draft.
Restrict the draft to just rookies: League >> Settings >> Configure Draft
Restrict the draft to a certain number of rounds, if applicable: League >> Settings >> Configure Draft
If your league has a taxi squad or an IR that owners use to free up roster spots for the draft, you'll also need to specify this: League >> Settings >> Configure Draft >> Count players on Injured Reserve/Taxi Squad.
Schedule a live draft time or begin an email draft.