The use of UAVs, in particular, micro VTOL UAVs, is becoming prevalent in emergency rescue and security applications, among others. In these applications, the platforms are tightly coupled to the human users and these applications require great flexibility in the interaction between the platforms and such users. During operation, one continually switches between manual, semi-autonomous and autonomous operation, often re-parameterising, breaking in, pausing, and resuming missions. One is in continual need of modifying existing elementary actions and behaviours such as FlyTo and TrackObject, and seamlessly switching between such operations. This paper proposes a flight command and setpoint abstraction layer that serves as an interface between continuous control and higher level elementary flight actions and behaviours. Introduction of such a layer into an architecture offers a versatile and flexible means of defining flight behaviours and dynamically parameterising them in the field, in particular where human users are involved. The system proposed is implemented in prototype and the paper provides experimental validation of the use and need for such abstractions in system architectures.