You can move one track to line up with the other in Audacity.
http://audacity.sourceforge.net/manual-1.2/tutorial_common_ed_1.html#tour2 That is just one i found there are heaps.
When you record in Audacity Select the recording source as Mic or Line just to record your
"vocals only" so you will have a vocal only track recorded in Audacity, then all you need to
do is add the wav, mp3, wma ect. to to Audacity and the move it to line up with the vocal track.
If you don't have an audio file just mute the vocal track in Audacity and now record
the music only select stereo mix for input.