If I understand your question right then try this:
First capture the video with the soundtrack from the camera. Then you may either mute the soundtrack or select Ignore event grouping and then delete the entire contest of the soundtrack.
Then you may record (with VMS Arm for recording and then Record through your mike or any other input on your soundcard) or by any other means build a suiting new soundtrack to your video.
If the audio source you have is recorded parallel to the videorecording you may have to syncronize video and audio i.e. at well defined sounds that you can "see" on the video track (clap etc).
It doesn't seem to be possible to record an AVI from an IEEE1394 AV inteface with an audio track coming in from elsewhere. I did find that an analog-USB2.0 converter would allow this because this converter itself didn't have an audio input (you had to use a dedicated audio interface as well), however you probably wouldn't want to go analog for the video just to achieve this!
So it looks like you have to do as the first reply suggested - which is a lot more flexible in the end, provided you didn't want to record the video and the altenative audio at the same time - but if you did, record the video to the cameras own storage and at the same time record the audio into a Vegas audio track. Then capture the video from the camera and drag it into the same project. They should be able to be lined up fairly easily.
The above is something I have not tried, but if I was taking the video close to a computer or had a good audio field recorder (the new Zoom H4 looks interesting) , I'd definately want to use a higher quality mic/interface for the audio than the cameras if I could.