Yup, any movie maker program should allow you to have separate audio and video tracks. When my Fraps records w/ sound the recorded .avi file has sound with it. When you import it into Vegas the Video and Audio of that .avi file are on their own tracks, but are linked together. That is if I move my video scene to 0:35 on the video track, the audio follows with it. Of course they can be unlinked if necessary.
I have the full version of Fraps, but the free version should work the exact same. It's only limitation is that after 30 seconds of constant recording, the video will turn to black and white. Sound recording should be fully functional. On the Movie Tab of Fraps, make sure record sound is checked, as well as Detect best sound input. Under Sound Device should be your sound card and sound input should be "What U Hear."
Do you have a dedicated sound card or does your computer have onboard sound?
As for your email, you cannot get the Fly-By sound effect (aka Doppler Effect, this is when a plane fly bys you and is soft in the distance and gets louder as it gets closer etc) from any 'recording' plane in an AH film. If you look at my movie I posted above, I'll be referring to the last section - the 109 vs p51. I was the 109 physically recording the flight. In the movie there is a part where the P51 zooms past the camera with the appropriate Doppler effect. Since the P51 was a different plan, the AH Film viewer will properly do the effect. But it is unachievable on the 109 since it was the recording player. Sorry, its the limitations of the Film Viewer. The only way to get around this would be to have the P51 record a film as well as the 109 record and then sample from each film.*
*You could do a volume panning across audio channels to simulate it, but I do not know the options and capabilities of your movie program.
It's okay to leave sound out of your movie. It's does add to the realism and excitement to the movie, but I'd say about 90-95% of the movies on my website do not have plane sounds in their movies.