Vorli,
I do not think that you will have much luck reading the signal with the digital I/O on a e-series board. The frequency of the square wave is 1-4 kHz, so you would have to be able to sample at atleast 100 kHz to get any kind of accuracy. To do that you would need strobed i/o. For example the PCI-6533 or PCI-6534 could do that.
To get good readings you would need to use a counter. If you look at the example program that I linked, you will notice that it only uses one counter. So you would be able to read 2 sensors per e-series board. Or you could buy a counter board. The PCI-6602 has 8 counters.
Carl L
National Instruments