It just runs your team in your absence. You can go into Management Console, uncheck the box and take control again.
Manage your big league roster? This includes lineups, pitching staff, disabled lists, signing draft picks, etc. This is NOT a recommended strategy for winning and is geared only at keeping your big league team healthy. It will not perform any offseason moves such as free-agent signing or coach hiring.
This setting is automatically turned on if you don't check your team for 5 full days (120 hours).