You might consider re-posting this question in the "multifunction IO" category of the "Measurement Devices" section. This newsgroup discusses LabVIEW Datalogging and Supervisory Control, which is an add-on package for LabVIEW that expands SCADA capabilities under LabVIEW.
That said, if you have a National Instrument E-Series data acquisition board or comparable, then the encoder signal can likely be used as an external scan clock to control the acquisition. I'm assuming that the encoder signal is 5V/TTL. LabVIEW ships with several external scan clock examples. Goto help >> Examples >> I/O Interfaces >> Data Acquisition >> Analog Input >> Continuous Analog Input >> Continuous Acquisition and Graph Using External Scan Clock. Also, your board's User Manual will indicate h
ow to connect your external clock signal.