I dont get it. Is this what you mean:
You move the clip to the timeline and you get the video line and the sound line, but the sound line only has you voice. When you save the project file, you lose audio line?

Have you tried to play the .avi file? If that only has your voice then you have same probelm that Im having, that the video recorder thing only records the audio-line from your mic and not the audio line of the game and your mic. Im trying to find solution for that myself too. On my topic of this problem, guy replied and said that there's topic about the problem in Project reality forums (www.realitymod.com if I recall right)

I havent used Movie maker too much for I dont like it. Too many clips and it crashes constantly, also the texts choices are kinda simple and you dont have too much options about the texts position etc.
My Movie Maker version is on finnish so my "translation" might vary. I'll add my translated version inside ()'s.
To mute the sound of your clip I'd do this:
Add your video clip in the project line thingy. Then from the toolbar click 5th one (Translation= clip) and select the 2nd one (Sound) and then click the first one (mute)
Then I'd Ctrl+P and save the file. After that I should have video file without no sound, so I'd open up a new project and add that to the project line of the Movie maker and perhaps add some texts and music to it.
To add text press 4th option from the toolbar (Tools) and click the 2nd from the list (Beginning- and Endtexts) from there you can choose where to put the text (you can move it's location afterwards) and edit it's backround colour text font, size, colour and animation. That's pretty much all options you have.

Movie Maker is pretty simple editor. I think you should get the hang of it.
After you get bored of it crashing all the time, I'd suggest you get bit more "professional" editor.
I use Sony Vegas 7.0 for editor atm. It's pretty complicated editor, for Im more used to use Pinnacle (dont remember version) which is mostly used for homevideos, thus simple editor for "older people" Video transitions of Pinnacle are bit childish imo so I turned to use Vegas.

BTW, if you are going to add music to your video file, do that last, because the Moviemaker tends to crash when editing the clips while having music file added. Atleast on my copy.

EDIT: Oh and BTW, you add audio files just as you add video files, just drag the file to audio track of the project.