I am a little confused on whether to embed swfs or load them when making apps for the iphone. Does anyone know what are the advantages of each (which is preferable to use)?
The answer is yes, you can embed SWFs, but that is not the only way. You can also use normal Loader methods, with everything relative to the main SWF:
var myLoader:Loader = new Loader();
// iOS apps act as if the main SWF is in a folder
// and the other SWFs are in the same (or sub) folders.
var url:URLRequest = new URLRequest("loadedSWF.swf");
myLoader.load(url);
addChild(myLoader);
myLoader.x = 50;
myLoader.y = 30;
With one caveat: during compile time (in the "Air for iOS Settings", in the "Included files" list), you have to list the SWFs that you want to be loaded, and they will get compiled into the IPA.
So, no you cannot call to external SWFs, but you certainly can access other SWFs using the embed
tag, or using (what might be called) IPA embedding.
Edit:
Since the question and title have changed a bit since I first answered this, here is a more generic summary. Apple does not allow loading local SWFs in the same way that you would be able to if using Flash Player on a website. There is no way to load an SWF (or anything else) using "relative" or "local" references in an i-device unless that content is compiled into the app. This does not apply to some types of "remote" SWF loading, and also does not apply to Actionscript "Native" coding, but that is not what the (original) question was about.