The way we have usually done it is that players stay in the same position as they were last year - regardless of whether the new ratings page gives a new position (Dion, take note of this).
If you would like to move a player to a new position, you must simply reference the new position as Drew mentioned (TSN, espn or whatever).
So if you signed, traded or just planned on keeping a player based on their position from last year, that is fine. The new ratings file was basically taken from an updated ratings file from an other league and is not meant to re-position players or to be the defacto position of each player.
If for some reason your player's position changes in the ratings update, simply make a request to move him back to his old position based on the old position (or a reference).
Damn, I hope that makes sense.