You should cut the clones before flowering the plant for best results. Ideally, you would cut clones from all your desirable plants just before flowering, then when the plants began showing their sex you would only keep the clones from those plants that were female. The clones have to be seperated out and treated with rooting hormone and placed into a seperate area on a 24/0 or 18/6 veg cycle.

Determining the sex is pretty easy if you just give it enough time. I accidentialy threw out all my females the first time i grew. The females usually seem to develop later, and the males will get very distinct 'balls' at the interesction of the side shoots and the main stem. Also, check the very top of the plants for signs, the tops sometimes show first.