OK kids,
first off, blu666.... do you see what the difference is here? Cool.
Next, I wanted to see if i was right, so I went home and checked it out. (I just so happened to have a show with two seperate sources of differing lengths.... go figure.)
The problem you are having is due to the fact that your sources are of different lengths. Track A is shorter than track B, let's say. So you line them up at first, and as the show plays, the difference gets more and more noticable. As you see, the shift is not necessarily noticable over 3 or 4 minutes but might be over 30 or 40 min. So what you are doing with the individual trax is fine, but you will have to slightly overlap the trax at the seams so that all the individual Track B's will fint into the whole of the shorter track A.
If you select the track (click in the box at the left of the waveform to highlight the entire track) and make sure playback is stopped, not paused, you can adjust the speed in the effects menu. This gets a little tricky, and i had to try it with two different compression percentages to get it right. (Make a duplicate of the track for eack different compression, then you can compare and keep only the ones you like.) It can help to find a kick drum or other specific spike in each of the two tracks so that you can jot down the points where they occur. Then, for the compressed track, find the same point and see how much it changed from the original. When you do it once, you will be able to say something like: At 0.4% compression, my beat moved 13 seconds. Then you can figure out how much more or less you want. (By the way... a negative percentage slows it down....)
If you do it this way then you wont have any overlapping to deal with (by cutting it out or leaving it as overlapped.. either way altering the original content).
IF IT SOUNDS MESSED UP... then maybe you want to go completely nuts (since I'm sure this mix is the only thing you have happening in your entire life) and shorten a little and then line up individually, thus decreasing but not eliminating overlap.
For the record, I am doing my project like this to get an audience recording (audio) to match the audio track from a video of the same performance. Why, you ask? because the film is synched with the original track, but it is crappy quality and i want to overlay the good audio while making it easy to re-insert it to the video. So I extract the audio from the camera, use it as a template for the right time duration of the show. I synch it up using the speed feature, mix the results making sure the resulting track is exactly the same length as the original camera audio, and then reassembling will be a breeze. (Right.)
*WHEW*
Peace out, gotta work sometime.
UJ