Found this in another thread....
I'm still testing but I fixed the NL to exact fan graphs / roster resource projections, Using 30 team control with a 26man roster when you start ST it auto fills out the 40 man. If you drop the added MLB players back down to the minors and advance to the regular season the lineups and rotations stick. I can only assume if I make the correct 40 man before starting a franchise then doing the same thing would work as well.