David;
To synchronize two boards trough the RTSI cable, you need to make one of those two as being the master and the other as the slave. The master board will generate all the clock signals while the slave board will use that clock as its new clock, instead of the internal timebase clock. Having that picture in mind, you will need to different RTSI operations, the first one routing, lets say, the CAN board clock signal, to one of the RTSI lines, and at the DAQ side, you will need to route that same RTSI line as beeing the AI Scan Clock signal, and specify the board as beeing clocked by an external clock signal.
Depending on the Software Language you are using to program the boards, you can find some good examples on how to synchronize multiple devices, either at
the NI-DAQ folder, or in the Labview shipping examples, in case you are using Labview.
Hope this helps.
Filipe