I haven't had this problem. Set it to USER for everything and it should be straight.
The NCAA draft import feature is broken. Plain and simple. Ratings from NCAA don't seem to translate properly to Madden along with equipment and body types.
The Madden generated aren't great but they aren't terrible either. I edited a few names here and there in my first two drafts to reflect actual rookies. Locker, Luck, Royster, so on down the line. Not a perfect solution but good enough for me.
This is the only way to do it. Letting the CPU resign, sign, and draft players defeats the purpose of controlling all 32 teams.