I would do it after the regular draft personally, let folks who want to use a regular pick on a kid first then do the rookie draft.
Originally I was going to attempt the same thing but as someone was asking for lists of eligible players myself and folks I talked with about creating one realized this was an error to do it beforehand and we did it afterward with a list. Of course thats just me/our opinions.
In any event once we implemented it we went with
"Any player who has not appeared in an MLB game before 9/1 of the prior year" Saves from counting innings, at bats etc and avoids folks who were just called up last year when rosters expanded. Some may say thats too extreme of a cutoff and again to each their own opinion!
Another league I am in that has had minor leaguers for a while goes with 150 AB, 75IP SP 35IP RP
In the end though as well as long as you set the parameters there are a number of websites with stats and service time that folks can also research. I was glad a person pushed for a list though, made it better for everyone with that list and holding it afterwards.
"And for that, we thank you!"
"I'm the man with the ball. I'm the man who can throw it faster than F***. So that's why I'm better than anyone in the world." - Kenny Powers