The bad news is that editing with CM and using the ingame editor at the same time will not work. The squads file is created by the game when you use the ingame editor, your changes are saved in it. It is based on the state the database was in when you made your edits.
However, CM saves directly in the db, which leads to conflicts with your squads file. To make the game use the CM edited database, you will need to delete the squads file. FIFA will then read the db again and create a new squads file. I know it sucks because you will lose part of your edits but as far as I know there is no other way. Had this very problem 2 or 3 FIFA's ago and only use Creation Master since then because it provides more editing options than the ingame editor.