How do Flight Test Engineers plan and execute sortie profiles?
Three main factors influence the flow of a flight test sortie: data requirements, test point priority and flight efficiency.  For example, consider a test sortie that requires evaluation of stall handling qualities. 


Data requirements specify which altitude, weight and cg, and configuration are required for each stall test point, for example.
Test point priority comes from the test team or test plan. One test point may be more important than others.
Flight efficiency refers to the need to minimize time between test points, minimize wasted fuel, and consider geographic position or airspace boundaries that may affect the test.


Balancing all of these things requires experience and judgment.  At the beginning of the flight, the aircraft is heaviest, so it makes sense to do test points that require heavy weight.  The second most important thing is to consider high priority test points. What points of high priority combined with heavy weight should be considered.  Finally, deciding the flight path that accommodates these two characteristics is the last factor.

This combination of judgment and knowledge and skill is difficult to describe accurately, and often two experienced professionals will come up with different, and equally acceptable, answers.