David,
The best way to syncronize these two PCI boards would be through the use of a RTSI cable. You've probably noticed the pin connectors on the top of each board -- they can be connected to share timing and triggering lines. You can find RTSI cables here:
RTSI Bus Cables.
To syncronize the boards:
The 6551 can be configured to output its onboard 10Mhz clock to RTSI pin 7 and the 5911 can be configured to phase lock with that signal. From the software standpoint, I would recommend that you configure the 6551 to export its onboard reference clock to RTSI (in LabVIEW, you would use the VI called "niHSDIO Export Signal"). Then, configure the 5911 to look for this reference clock on its RTSI connector using "niScope Configure Clock." Finally, configure the boards to also share a start trigger. Configure the 5911 to wait for a start trigger pulse on another RTSI pin and likewise the 6551 to output a pulse on the same RTSI pin when it begins generating.
I hope that this is helpful to you.
Regards,
Alan L
Applications Engineer
National Instruments