Hello,
Could you please explain what type of counter operation are you interested in doing? That would help me in suggesting something.
But if I roughly understand what you are saying here, you can use a same clock to provide as scan clock for analog input and then use that clock for the counter. But depending on what counter operation you are trying to do will decide whether that clock be provided as source or Gate.
You may take a look at examples provided at the following location too :
Measurement Hardware Sincerely
Sastry V
Applications Engineer
National Instruments