Have a look into Third example of thistutorial. You can configure as many pins you want to any of the edges.
It depends is the counters are separate or combined. If counters are separate you can reuse same code to increment them, but if they are shared (like all them increase same variable) then you have to perform some locking on the variable to prevent data corruption.
If you still have problems message me so I will try to put down some example for you
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