First, absolutely avoid recording through a webcam's mic, that's the worse thing to do
I don't know if you can get the recorded audio files from amplitube to the computer, but if you can, you can then synchronize the file with the original song (with bass mostly EQ'ed out). As for video, you need to use some video editing software to cut the sound from your recorded video and then sychronize your final sound file with the video.
That's not the most efficient way to do it, but that's the way I do it.
The best way of course is to have a sound card with instrument input and record everything at once and have a perfectly finished video, but this takes some preparation, and also you can't work on your sound afterward.
[url="http://www.youtube.com/watch?v=knhJ2GZ248Q"]http://www.youtube.com/watch?v=knhJ2GZ248Q[/url]