Downside of overlapping graphics and text

Ok, so here is my problem. If I use many small audio files and break the lesson into small chunks I get the IE default click on each page change or sometimes a flicker for the end user. If however, I use flash audio and events to change what graphics and text boxes show I get a seamless look on the production file, but a mess for editing, with 5 stacked graphics and text boxes. Any suggestions on a happy medium or better way to minimize page changes? I also use events in the audio file to determine pacing and change to the next page or section so that I can use pause and play buttons without restarting the audio from the beginning.