VG,
If you want to save the settings for your DAQ devices, the easiest way to do this would be to set up the acquisition in a task in Measurement and Automation Explorer. You can then export these settings by going to File >> Export.. You can then export it in a few different file formats. Then, instead of using the DAQ Assistant in your LabVIEW code, you would just use the DAQmx Start, Read, Stop and Clear VIs to control the task's execution.
I think that this would be the best way of accomplishing the task, since setting up a task is essentially the same as setting up the acquisition in the DAQ Assistant. Other than this, you would need to develop your own Express VI that would allow for storing the settings of the acquisition, which would be pretty involved.
Here are a few links to using the DAQmx driver in LabVIEW, they should help you get a better understanding of how the driver works and how you can set up your acquisition using tasks.
Learn 10 Functions in NI-DAQmx and Handle 80 Percent of Your Data Acquisition Applications
Complete Data Acquisition Tutorial
Getting Started with NI-DAQmx: Main Page
I hope this helps.
Brian Coalson
Software Engineer
National Instruments