You need to use the RTSI bus to route one board's clock signal to be the second board's clock signal. By doing that, you will have the same signal clock timing both boards, which will make the synchronization hardware timed.
You will need to have a RTSI cable connecting both boards together also.
The best way to go about this is to open the Labview examples that show how to synchronize multiple devices. You can apply the same idea to your board.
The examples can be found at Search Examples->I/O Interfaces->Data Acquisition->Multiple Device DAQ Examples.