Sugus,
In LabWindows/CVI or NI-DAQ with other programming languages, you program the DAQ-STC with GPCTR function calls. In particular, to configure a DAQ-STC counter for up/down counting, use the GPCTR_Change_Parameter function with parameter type set to ND_UP_DOWN and parameter value set to ND_HARDWARE.
Once the DAQ-STC is properly configured and your software program correctly retrieves the count from the counter, you can convert the count into rotation.
I would recommend to take a look at the following page for more detailed information and example programs about DAQ-STC and Quadrature Encoders
http://zone.ni.com/devzone/devzone.nsf/webcategories/75CA12ECD25F39A78625679000743752?opendocument&node=DZ52326_US
Good luck with your application!