Hello Chris,
If I am understanding your question correctly, you are trying to determine the best samples to read for your application. To best understand what will work best, I think it is easiest to explain exactly what that value is. The only thing that you really care about is that the Samples to Read value determines the number of samples returned each loop iteration. It is a blocking function, so if the value is high, everything will wait until that number of samples are available for the loop iteration to end. It does do some buffer sizing stuff, but DAQmx takes care of all of that behind the scenes. We usually recommend that the Samples to Read be set at about 10% (or greater) than your sampling rate. This usually takes samples out of the buffer fast enough to avoid problems. However, because you are writing to a file each loop (which takes significant time) you probably want higher than this.
Take a look at
this article. It describes the different errors people most often get when it comes to buffer stuff (and Samples to Read) and should clear things up.
So in short: Your 1000 Samples to Read should be fine. So would a higher value.
Neal M.
Applications Engineering National Instruments www.ni.com/support