You can definitely use two PCI-6031E devices simultaneously to acquire from 64 differential channels.
If you aren't needing synchronization between the two devices, then you could create a program that continuously acquires from both devices. This is a very easy procedure. There are many examples that continuously acquire from a single device. You would just need to duplicate that code for the second device.
If you are wanting to syncronize the sampling of the two devices, you could use a Real-Time System Integration (RTSI) cable. Using a RTSI cable allows you to share signals (clocks, triggers) between devices. The links below help explain RTSI in more detail.
What is RTSI?
http://digital.ni.com/public.nsf/websearch/A120195AAAA9222A86256C69007C8B27?Ope
nDocument
RTSI Bus Cables
http://sine.ni.com/apps/we/nioc.vp?cid=3544〈=US
I've included links below to programs that integrate multiple DAQ devices for your reference. I hope this helps.
Sharing an External Scan Clock with RTSI
http://sine.ni.com/apps/we/niepd_web_display.DISPLAY_EPD4?p_guid=B45EACE3ED7F56A4E034080020E74861&p_node=DZ52336&p_submitted=N&p_rank=&p_answer=&p_source=External
Acquiring Data Using a Digital Start Trigger Synchronized Across Multiple Boards Using RTSI
http://sine.ni.com/apps/we/niepd_web_display.DISPLAY_EPD4?p_guid=B45EACE3EE9D56A4E034080020E74861&p_node=DZ52336&p_submitted=N&p_rank=&p_answer=&p_source=External
Regards,
Todd D.
