The "Position Assignment" pop-up page from the "Edit Rosters" page does a good job with that. If you hit "Show Recs", it will suggest primary and secondary positions for a particular player. You can modify the suggested positions as you wish. But if a guy is a LH thrower, it will never recommend 2B, 3B or SS as a primary or secondary position.
Then, on the lineups page, when you click in the "Pos" pull-down, you'll see the primary and secondary positions noted. If your 75/65/55/55 LF doesn't have 2B noted as a secodnary position, don't play him there.