Hi Falk,
You have a couple of options in implementing a square wave generator.
1) If the timing specifications on your square wave can afford some skew, you can use a software timed loop to constantly update a digital line on your board. I would use the built-in software timers of your application development package (For example, Wait Until Next ms Multiple.vi in LabVIEW). A software timed loop is however dependent on your system speed and your OS. Typically, you won't achieve speeds much greater than 500Hz using this method.
2) You can use register-level programming (RLP) to access the timer chip used for pulse generation (82C53 timer chip). You can even program the digital I/O chip for strobbed output. But this is all done through register level
programming (see page 4-3 of PCI-DIO-96/PXI-6508/PCI-6503 User Manual). To perform register-level programming you can use Appendix B of the manual. This functionality is not supported by the NI-DAQ driver API.
PCI-DIO-96/PXI-6508/PCI-6503 User Manual
http://www.ni.com/pdf/manuals/320938c.pdf
3) You can purchase a Basic Multifunction DAQ board at a reasonable price that has on-board timers to create your square waveform.
Hope that helps. Have a good day.
Ron