I accidentally did something similar - got the date of my live draft wrong, so basically got my team autodrafted to everyone else's live picks. I think the system just picks for you in terms of highest salary player available that won't put you in jeopardy of the cap (my first pick turned out to be Kershaw).
I think I ended up only keeping 4 or 5 of the drafted players, and had to compile the rest off the scrap heap. Missed the playoffs, but still had 91 wins. I think what I really got out of it was that no matter how many players you miss on, there will still be enough takent available to cobble together a competitive team...real deep analysis, I know, lol. Mighta helped that it was a $90M cap too.
Here it is, as an fyi:
http://onlinegames.strat-o-matic.com/team/1382221