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Creating Watchdog Timer Loops

I have a USB 6259 running with LabVIEW 7.1.  I realize this does not have a built in watchdog function, but I have a piece of hardware that I plan to attach to the digital output of my USB DAQ device that will be my watchdog timer.  I am uncertain, however, of how I can program this.  I need it to be on for 5 seconds, then off for 5 seconds, continuously.  Will doing this slow the rest of my program down to only loop every 5 seconds?  If so, I can't have that.  I don't know where to begin to program this loop.  I have just become confident in my ability to program using analog in/out, and now the digital is throwing me off.  My process will be acquiring data, and controlling a couple pumps, which is why i need the shut them off in case of a computer failure.  Help is appreciated!  Thank you.
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You can just add a parallel loop to handle the digital output to the watchdog. 
This won't slow your main loop to 5 seconds; the loops will be independent.

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