How it works:
If you have missions turned on: In the game if you constantly have an active mission you will see no difference. It is only if you do not select a mission at the start of the game or if a mission is over and you have none active. After a while if no missions are selected the computer will assign you one. Note: you definatley do not want the computer to assign you one.
If you have missions turned off: You can select missions as and how you please, the only difference is if you decide to not use missions at all or let all your mission expire with no new one selected, the computer will not force one on you.
My recomendation turn them off and do not use them.
As to the specifics of this thread: If you selected to have them on when you started your scenario, then you cannot turn them off, when reloading. You can edit your save game to turn them off however.