I have completed quite a few of the main missions in Prophecies but may have not completed the bonus missions associated with each. Is there a way to see which mission bonuses you have/haven't done?
Yep, On your main map, The mission areas you've completed with the bonus will appear with 2 swords through the shield. The one's you've only done the mission on will have one sword that goes from Upper left to lower right.
Yes press M
If its a shield icon it's not done
If it has a sword top left to bottom right the mission is done
If it has a sword top right to bottom left the bonus is done
If it has 2 swords bonus and mission are done