I don't support the idea of a 3 day draft, but if I had to do it, I'd set it up as Day 1: First Round, Day 2: Supplemental Round and Second Round, Day 3: Rounds 3-25.
There's rarely anything of value left after the second round, save for a few guys available at the top of round 3, and those are usually low durability/stamina/health type players who slipped due to concerns with how often they can play.