I have always understood flatness to be a best fit feature unless tied back to datums (which I have not seen). As such, it is important to adjust the part until you have the least amount of difference in your sweep, this can be done in either orientation as long as jacks are used. the important thing is to establish your zero at the low point (if using the top surface, which is easier in my experience) after balancing the part to the least variance.
// would be measured if you balanced the bottom of the piece to the least variance then measured the top (or vicea versa). If you are balanced on the surface you are evaluating then it would be flatness.
A lazer scan would be the easiest way if it is available but if you need to use the indicator technique then this is the best way i have found.
Hope this helps.
Mark