This device and connector block should work fine with a quadrature encoder. I recommend that you look at the video tutorial located here.
The specific configuration will depend on what you are trying to measure (edge count, frequency, period) and will also depend on the frequency of your signal. If you create a task in MAX for the 6033 with the BNC connector block, the settings tab will indicate which channel your signal should be connected to.
Please repost if you have a more specific question.