Hi balajkasthuri,
The best way to perform this is to use the frequency generator (freqout) of your 601x board. Your board only has 2 counters but it also has a frequency generator that doesn't use the counters. It is an output found on the freqout pin. You can choose to have a frequency of 10 MHz or 100 kHz divided by any integer between 1 and 16. This means you can create a pulse train of known frequency and known period and use that into the source or gate of your two counters depending on the frequency measurement method you are using.
For example, assuming your two signals are much faster than the freqout signal, you can apply the freqout signal to the gate of a counter and have your signal feed the source. The number of counts you get in 1 pulse
width of the gate (which is known since it is the frequency you generated) will determine the frequency of your signal.
Otherwise, if your signal is much slower than 20 MHz, you can simply use the 20 MHz as the source of the counters and perform a simple period measurement on your signal. You would then take the inverse of your period measurement.
Anyway, using the onboard frequency generator will give you the flexibility you need. I have linked below a useful tutorial describing the 3 typical frequency measurements. Hope that helps. Have a good day.
Making Accurate Frequency Measurements
http://zone.ni.com/devzone/conceptd.nsf/webmain/CD2C8AAED8FA59A486256C230078FE75?opendocument
Ron