Amber,
The timing that you have implemented in you VI only affects whether the waveform you are simulating is on or off and does not affect when that waveform is actually written to the device.
If we have a sample rate of 1000 Hz this means that we will have 1000 samples per second. We can then set the Samples To Write setting to 10000 samples, which will generate the signal for 10 seconds. We can use this to our advantage to generate or acquire for a certain amount of time. I have created a simple example to show how this is done.
Regards,
Chris Delvizis
National Instruments