Why do you want these readings? Are they used for control (such as to determine when to stop the kiln) or are they used to document the MC for subsequent grading or users? The purpose will determine the actual technique.
IN GENERAL
The first step is determining how the hot readings relate to cool readings. Generally, the hot readings are adjusted and each mill has their own adjustment factors for species, thicknesses, etc.
The second step, is that for a good statistical estimate, about 32 readings are necessary, avoiding unusual pieces of lumber (top of the stack, thin, edge pieces and so on). Obviously, sampling from all the stacks, not just the low ones is important.