There is a good discussion on using quadrature encoders with the E-Series DAQ cards at the following location:
http://zone.ni.com/devzone/devzoneweb.nsf/opendoc?openagent&36BD71244BB26FC886256869005E541B&cat=75CA12ECD25F39A78625679000743752
One way to do what you are talking about is to have an encoder pulse drive the DAQ clock. You can trigger the acquision to occur at a specific time (i.e. position) after an index pulse. You should try to get to know the low-level DAQ routines intimately before trying to do this. Look at the hardware triggered DAQ for a start.
Another approach is to use a motion control card to acquire the encoder position and set breakpoints to trigger DAQ events.
You will also want to take a look at how RTSI works if you want to route
trigger and timing signals between cards.
-Jim