This post is for the newbies more or less. Position players are a tricky lot sometimes. They may have their skill set to one position or multiple positions. They may or may not carry the skill set needed for a position. Alas, here to the rescue is how to change that interesting bumbling.
To change a position players primary position or secondary set, click on GM's Office-Roster Management-Edit Rosters. You can go through each roster and perform many functions as outlined at the bottom of the page. Any function selected and action taken on a player will give you a second chance for you to execute the function. It will not happen until you submit the action for processing. So be sure that is what you want to do. Be warned that you should thoroughly read the help section on this, especially the GM's Basic.
As for changing a players position, click on the position next to the player involved after that interruption. It was brought on by the wife, "What's this for?", her version of 'Are we there yet?'. Anyway, it will bring up a pop up mini page that outlines the so called minimums for a position along with the players current and projected ratings. The last line is for the primary and secondary positions. You can change them manually or select one of the buttons below. I normally go with Show Recs (proj) and edit if not to your liking before hitting the Save button.
The reason for this is to easily set up lineups thru the Management Console so you don't have to do it manually, it can be such a burden in the minors. If you use the Management Console on the ML team, at the beginning of the season is okay, but trust me, you will need to go edit the lineups and pitch settings manually afterwards.
When a player becomes injured and needs to be put on the DL, holes will exist in the rest, defensive replacements and pinch hitting settings that need to be addressed. I am always forgetting those.
Also players playing a position that is not on their resume brings on 'out of position minuses' I believe in the sim. Whether he can actually play the position or not.