Sable,
Today, you can only have one mission active at a time. It can only contain 8 different 'flights' with I don't know how many Aircraft per flight. I'm thinking it can handle 3 digits, but never tried.
You can, however, edit your mission, even after it has started and change flight information, waypoints, loadouts... etc. ( planes that have already launched will not be affected by the changes, except their waypoints will change if you change them. )
You can also build, save, submit, change missions while flying.
This includes start and end times.. for each flight, even. So, you can set a start time and an end time hours in the future, then, while the flight progresses, make changes and resubmit as necessary.
Hope this helps..