With respect to stains that don't come off with soapy water and bleach -- it depends. It depends on how big and obvious the stains are, and it depends on how well the stains (unwanted) are covered by the stain (wanted) you choose. The dryer the wood, the more stain it will absorb, and a better off you be. Therefore if you can wait two or three days, you are better off. I prefer stains that are thin and watery and are mostly absorbed by the wood, rather than thicker opaque stains that leave a layer that can peel. The thinner stains seem to wear less in high-traffic areas. Based on your comments about peeling, I suspect you are using a heavier stain. Therefore, that necessity to restain the whole deck, rather than high-traffic and sun-drenched areas, is a question of aesthetics.