counter with flip flop

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"how we decide which flip flop is used for counter"

It depends on the sequence of counting. Asynchronous mode is fast to wire up and requires less additions to it than Synchronous mode .. You just make the JK flip-flops in Toggle mode (J and K to High) and put the 0th bit output to the 1st bit Clock, and you're done with your 2 bits counter.. (Look at the schematic provided by Reloadron for JK flip-flops)

And then, it depends on the sequence you want to count, propagation time, etc.. For your case, I suggest you go with JK flip-flops in Asynchronous mode.
 
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