If the draft gets set to auto, does it still pick from your list if you have players on it, or is it full auto with drafting determined by the AI? If it picks from your list then it should work for everyone as they can just load their lists up with some guys they want and cross their fingers 
Well, statslab will indeed draft off your list until it runs out of options and then it will pick what it thinks is the best available player.
There are two problems with this, though. (1) It doesn't take into account what you have on your roster already, so you could wind up with 75 catchers and no outfielders and (2) Matt will be left manually inputting all 125 rounds so...
I strongly recommend we use the auto draft function IN-GAME after we finish manual picks. This will mean (1) our teams will be more balanced by position and (2) Matt will only have to manually input 25-40 rounds of picks. As a commish, I can say that this will take quite a while, although at least there are no traded picks to worry about.
With that in mind, I wouldn't take the time to put the whole pool into your list unless you have an easy sorting method and it doesn't take you a whole lot of time.