Knji,
Counters are definitely the means to accomplish your task. There are two 24-bit counters on the PCI-6036E. If you just want to count pulses, you will want to use a simple event counter example. There are also examples that measure frequency, period and pulse width. If you have the NI-DAQ driver installed these examples will be included with LabVIEW or LabWindows/CVI, and you can browse or search for them at Help>>Find Examples. If you want C/C++/VB examples, you can find them in the following directory:
C:\Program Files\National Instruments\NI-DAQ\Examples
Hope this info helps!
-Alan A.