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We try to automate the resuming of a mission. If there are specific cases that are not working for you please let us know and we will try to cover them.
If a mission is stopped part way through we try to make it recoverable in a lot of ways.
At any point that you manually want to bring the aircraft in for some reason just try to close the app first. We have attempted to make it easy to recover from an app crash but that makes it a bit harder if you are doing things manually.
Generally we recommend saving the mission so you can see where it is when doing a layout for redoing sections.
The next version will have a lot of features to make this easier to do.