I don't understand your question, but note that BufferedReader can read more characters than you ask for and store them up for later requests; that's what "buffering" means. Therefore you should never, ever create more than one BufferedReader for a given stream, and furthermore, once you create a BufferedReader for a stream, all reading from that stream must go through that BufferedReader. If you don't follow this advice, data will seem to mysteriously "disappear."
Finally, for the special case of System.in, which has its own buffering, it makes sense to turn BufferedReader's buffering off, anyway, or other weird stuff can happen. You do this by supplying a second argument to the constructor, the number '1'.