Hi Prashanth,
The trigger line on the J2 connectors are basically RTSI trigger lines and can be used to synchronize across different cards on the bus. This is can be called via the regular DAQmx API, and example VIs can be found in the Example Finder (Help > Find Examples) and browsing to Hardware Input and Output> DAQmx > Timing and Synchronisation.
However, if you are looking to synchronise all your readings based on one trigger, you will need to use the Star trigger, and for this you will need the PXI-66xx cards. You can find example VIs for using the Star trigger lines in the LabVIEW Example Finder in Hardware Input and Output > Timing and Synchronization. You will need to have the
NI-Sync drivers installed.
Also, what sort of cards are you going to be using? If you plan on using FPGA modules, your question might be better answered on the FPGA forums.
Hope this helped!
Rasheel