For this situation, I recommend using responsive layouts. Your document will change based on the width of its container (in your case, the iframe). If you pair this with flexible layouts, then you can fit multiple widths.
Whenever you load a scene, the main timeline will run. If you have an intro animation that you don't want to run each time, just make sure that intro scene is first. You can then switch to the second scene by using a timeline action. Alternate timelines are also useful for changing scene load behavior (or running an animation only on that scene's first load).