You could go the route as suggested by Ryan which would work
well, but
it might prove to be more work than necessary to take your
measurements. Your DAQ device has direct encoder support on each of the
two counters. What this means is that the device can accept each of the
signals from a single-ended encoder - A, B, Z (Index). If you are using
an encoder with similar signals, then I'd recommend either opening up a
position measurement example from the LabVIEW Example Finder, or
configuring a DAQ Assistant according to the specifications of your
encoder and then having the configured DAQ Assistant generate the code
for you. The examples in the Example Finder can be found by browsing to
Hardware Input & Output >> DAQmx >> Counter Measurments
>> Position. If it's the raw 11-bit digital data that you'll need
to transfer, then use the recommendation that Ryan suggested.