nnio,
Connect phase A of the Quadrature Encoder to the SOURCE of the counter to be used and connect phase B to the corresponding DIO up/down line (DIO 6 if phase A is connected to the source of counter 0, or DIO 7 if phase A is connected to the source of counter 1).
With this method you can connect phase A and B of your first encoder to counter 0 and phase A and B of your second encoder to counter 1.
How Do I Use a Quadrature Encoder with My Data Acquisition Board?
http://digital.ni.com/public.nsf/websearch/C6C6632A54DBA7DD86256275005E18E2?OpenDocument
Quadrature Encoder with DAQ STC (E-Series Boards)
http://sine.ni.com/apps/we/niepd_web_display.DISPLAY_EPD4?p_guid=B45EACE3E9AD56A4E034080020E74861&p_node=DZ52326&p_submitted=N&p_rank=&p_answer
=&p_source=External
Regards,
Justin Britten
Applications Engineer
National Instruments