You can connect an encoder to a PCI 6025E and to a SCXI chassis at the same time with out any problems. The SCXI chassis uses DIO lines 0, 1, 2, and 4 to control the chassis.
If you are using a SCXI chassis, I would recommend using a SCXI 1180 (feed through panel) with the 1302 terminal block to gain access to the pins required to attach an encoder. If you are not using a SCXI chassis, you could use a standard SCB-68.
Here is a link that discusses how to connect the encoder in great detail.
http://zone.ni.com/devzone/devzoneweb.nsf/opendoc?openagent&36BD71244BB26FC886256869005E541B&cat=75CA12ECD25F39A78625679000743752
For the most part connect your A line from your encoder to GPCTR0_SOURCE (pin 37 on a SCB 68) and your B line to DIO 6 (pin 16 on a SCB
68).
Here is an example in LabVIEW and a KB that explains how to program this in more detail.
http://venus.ni.com/stage/we/niepd_web_display.DISPLAY_EPD4?p_guid=B45EACE3E9AD56A4E034080020E74861&p_node=DZ52326&p_submitted=N&p_rank=&p_answer=&p_source=Internal
http://digital.ni.com/public.nsf/websearch/C6C6632A54DBA7DD86256275005E18E2?OpenDocument
Note: There are several examples of how to use an encoder with the E-Series devices (DAQ-STC) on National Instruments web site in different programming environments. Also, the 660x (DAQ-TIO) devices are the recommended devices for performing encoder measurements.
Joshua