The easiest way to combine two waveforms is to use the Build Array.vi. Below is a screen shot of how you would write two waveforms to a file. Just take the waveform, build a 2D array, then save that 2D array to a file.
If you need to parse out the waveforms after reading the data, then just use the Index Waveform Array.vi found in the Waveform subpalette.