If you are writing a single waveform at a time to the save waveform to file VI. You are are adding each new waveform on to the existing waveform, creating one big waveform. What you will need to do is write the waveforms in a manner of arrays (which the help in LV6 gives information about with the waveform file i/o VIs).
I think that you will have to read the existing file add the new waveform into an array with them then save it to file. Then on the read waveform(s) the output will allow you to take each waveform and display it seperately.
Doug
