the dept chart is basically the drop down menus under where you select your starting team. Basically if you choose not to put a player in the depth chart and pick the option "coach picks from depth chart" he will only use players that you have added to those drop down menus. So ye basically coach picks from the depth chart option means the coach will play what team he thinks is best based off the players you put in the menu.
if thats not right i've been believing the wrong thing the entire time and need help too :(