Transitions when using only actionscript for Animation

Hi. I’ve read the transitions tutorial and understand how that works, however, the site that I am building uses actionscript for its animation rather than timeline effects (for the most part). I was wondering if anyone had any suggestions on creating smooth transitions between external swf when the animations are done in actionscript?

Right now in my external .swf I have two frames, the first frame is the intro the second is the outro. The only difference between the two frames is the actionscript is reversed from fading in to fading out (etc.) on the second. There is no “midframe” per say, it just stops on the first frame because there is a “stop();” on it. When the user clicks out of that section it just moves and plays the second frame. This works, however I fear that that method will get me into trouble later on. Is there a better way of doing this?