Yes, you can load any number of SWFs that interact with each other (except in iOS of course). You just need a parent container with the logic to get any messages to where they are going. Maybe I don't understand the question. Is there a specific design decision in your app that is preventing you from doing so? What problem are you trying to solve, specifically?
Why wouldn't it work with iOS, doesn't the AIR runtime allow for flash based files to run? In the app specifically I don't know how to load all the files, do I use a SWFLoader and load all the files at the same time? Thanks for the help by the way, I really appreciate it.
AIR does allow such a thing, but Apple does not. It is a violation of the iOS Developer Guidelines to load executable content at runtime. Assuming there is no code in the SWF [most of them have at least a call to stop()], then it should work in iOS.
To load multiple SWFs, just use multiple SWFLoader instances and place them on the display list. It helps if your loaded SWFs implement a common interface so you can interact with them in a generic way.