They count as draft picks. When the draft room loads, they'll be pre-selected. You cannot tell which player you want in which round though. If you put 5 guys in, they'll take up their first 5 picks.
Don't be confused with a snake draft. If you put 5 guys in, the 6th round normally in a snake draft goes from 12-1. The first guy in the draft will get to pick first, so don't make the draft order opposite as I thought I used to have to.