You can write individual channel to a file by splitting up the data from your DAQmx read VI using Split Signals. This can be found in the Function Palette » Express » Signal Manipulation » Split Signals.
This will split your data into each indivudual channel that you are reading. If you want to write a group of channels together into a single file you can bundle just those channels back together with Merge Signals, which is found in the same palette
I already knew about the split and merge. I needed a way to id each channel because sometimes the channels being used will change. The split and merge methods are to "hardwired" for my app. Is there a way to use them dynamically? Ideally I would have a list of possible channels in the group and then I would check to see which ones are present. I have found on method that is working so far. I assign names to the channels in the task and then use index waveform array by channel name. I then merge those signals. I haven't checked to see if it gives an error when a signal is not found though.