Hi Jaap,
The trick is to use the RTSI Connect VI. This, combined with a RTSI cable, allows you to share the clock between the two boards effectively making them appear as a single 64 bit device. Here is an example program.
http://sine.ni.com/apps/we/niepd_web_display.display_epd4?p_guid=B45EACE3E18956A4E034080020E74861&p_node=DZ52336&p_source=External
I hope this helps!
Russell
Applications Engineer
National Instruments
http://www.ni.com/support