The one I did eons ago was setup where for players you are keeping, you lost the pick in the same round as the round players were picked the previous year (e.g., if you picked Aaron Rodgers the previous year in the 1st round and you decided to keep him, you'd lose your pick in the 1st round for this year). I don't remember what we did for waiver pickups.
I just checked my team, I have Green, Bryant, and ODB sitting on my roster. I'd completely forgotten about that since the rest of my team was atrocious, not to mention Green missing several games.