Hi JS. Overhead squats (OHS) are a great overall exercise, probably doing more good for the cor, shouldle, hip and ankle flexibility than overall leg strength. standAPART mentions them in his article "The battle of gravity and the TVA: in the visitor article section. I would recommend anyoneand everyone read it.
As to the OHS itself, well, I would recommend doing them every session with a PVC pipe or unloaded bar every session for 3X8 or so reps as part of the warmup. This will loosen the whole body up as well as develop flexibility. Now, how to use them as part of your actual workout. If you are using a squat day, as I suspect, and trying to up your poundages, just put them in on that day. Sets, reps are up to you. If you are into actual OL, sets of 3 or so will work. For general fitness, sets of 8 or so are good.
Here is a good article on the subject.