I dropped my QTREF file into Sorenson Squeeze and put the DVD_NTSC_Lg compression on it and it came out with an .M2V file. When I play this file in my Windows Media Player I only have video and no audio. I thought it may have seperated the audio and video tracks, but I can't find an audio file to go with my video. Any suggestions?

Sounds like you created an Elementary MPEG-2 Stream.  If you want them to be embedded together, you need to specify a Program stream.

The audio that corresponds to your m2v is probably a wav or ac3 or something like that, (depending on your settings)

 You could use the wav or aiff that was exported with the QT reference for your audio.