I've connected oscilloscope in dual channel mode, 'A' to input and 'B' to output and both the wave forms are showing absolutely fine , but the two pointers given on a graph can only be move on the wave of channel 'A' :/ how to use the second pointer on channel 'B' wave form

 

Are you talking about the time-axis cursors? If you click on the wave you want to analyze the cursors will be referenced to that waveform.