I guess controlling was the wrong word to use. What I meant was would it be possible to send the CM way points for a route they wanted the AI formation to follow?
I understood what you meant.
Think of the mission as a predefined set of waypoints with a target speed and alt and behavior associated with each transit to that waypoint.
Once you kick it off, the AI are going to follow those waypoints at the specified alt and speed and drop where you tell them.
Before it can be uploaded and run, it has to be "compiled" and after that can't be modified without recompiling and re-uploading a new one.
So, because it must be compiled by an offline tool, it's really not feasible to define one on the fly in arena or alter one after it's been uploaded to the server.