Hello,
For doing any type of testing with your board, first of all the board will need to pass the Test Resources in MAX.
Here is a link that explains how to troubleshoot common problems (like the one related to "The Device is not responding to the First IRQ level"):
DaqCard Installation(PCMCIA)Regarding the use of the counter/timers, I advise you to take a look at the LV shipping example: Count Edges (DAQ-STC).VI. In general, you will have to connect the TTL signal coming from your device into the source pin of Counter 0 or 1.
Good luck with you application!