This will sort it self out given that your door to quarter panel gap is set right with no worn hinges, pins and bushings, and the door glass is set right fore/aft with proper seal to the weatherstripping with no wind noise or water leaks, and the stainless strip is fully seated and bonded to the glass edge.
Long story short, don't worry about setting an overlap, it's the things mentioned above that matter and will determine it.
Door, and door glass adjustment is covered in the volume 4 Body service manual.