I'm a little confused and so you might need to explain your application more thoroughly.
Are you trying to use one counter to count multiple signals? From your statement, it seems that you have multiple TTL pulses coming in and you want to use a single counter to count each pulse.
What frequency do the digital signal(s) have that you are trying to measure? If their frequencies are fairly fast, you won't be able to reconfigure (reset) the counter before getting the next count. This is because, resetting the counter will happen in software and that will be system dependent.
If you are needing to count muliple TTL signals, I would suggest to look at one of our counter/timer devices (NI 6601, NI 6602) linked below. Using a counter for each signal would be the
optimal way to count multiple counters.
I hope this helps. Let me know if I'm completely off-base.
Counter/Timer Devices
http://sine.ni.com/apps/we/nioc.vp?cid=4553〈=US
Regards,
Todd D.