I have not looked at the tutorial, but what you need to do is build it inside a movieclip so that you can control the layer it occupies. Try taking whatever code you have for it and plant it inside a movieclip and see if it plays out properly without any need to tweak it.
add an empty movieclip to your lowest layer. assign it an instance name, eg bubbleParent.
then when you add bubbles, use:
bubbleParent.attachMovie(...); // if you're using attachMovie
bubbleParent.createEmptyMovieClip(..); // if you're using createEmptyMovieClip
Unfortunately putting the script inside of another movieclip resulted in Flash crashing on me multiple times. Go figure! The good news is adding an empty movie clip seemed to work just fine. I had to alter the position of the empty movie clip in order to make the bubbles appear in the proper location, but it seemed to do the trick. Thank you both for taking the time to help!