Ideally the tuning move should reach the maximum speed the machine will run at, however you should gradually work up to that when tuning, just to avoid causing any prolonged wild oscillations if a change in PID settings makes things badly unstable.
KFlop lets you do two different types of moves. A block step move, and a move limited by the Velocity, Acceleration, and Jerk settings.
The block step is an instantaneous command (i.e. Acceleration and Jerk settings are ignored) to move the requested position amount, which you use to determine just how quickly the system can accelerate, and how quickly it can handle peaks in command, but it's brutal on the machine.
The VAJ limited move is more like a move you'd command during G-Code running, which is what you use for normal tuning.
What you're looking for when tuning, is for when things become unstable, then backing of a bit.
Ideally after sudden change in requested position/speed, there should be a short peak in output, which should quickly settle down with minimal oscillation.
If you have no peak, then the output isn't being driven hard enough, and you're following error will most likely jump up until things catch up.
If you have a peak, that is followed by endless oscillations, then best case scenario the following error can be pretty low, but the servo will be continually oscillating to stay on position, and in the worst case, the servo will be wildly oscillating with a huge swing in following error.
You're aiming for a compromise between the two.
And I've just remembered there's a guide on the Dynomotion wiki -
http://www.dynomotion.com/wiki/index.php?title=Main_Page#Axes_Servo_Tuning_and_Trajectory_PlannerSome of it won't apply, but the underlying process will be very similar.