I'm guessing you are prewashing your fabrics (as would I). My method is to hang the fabric with selvedge edges together. You will see the puckers. I then lay the fabric flat on the table and smooth the fabric from the folded edge to the selvedge edge until there are no puckers. I then ignore where the selvedge edge or the cut edge falls. I trim one side of the cut edge so both layers are even. In your case, since you are double folding, I would follow the same smoothing process with the second fold (after pressing that first folded crease with LOTS of starch) and before trimming the one edge. Then use that cut edge to start my measurements.