Generally, your app will be stretched to fill the larger screen.  This table shows the various devices and their screen sizes. 

When you upload your app, you have the option of specifying which screen size your app is targeted for.  In the dropdown for 'Display Size?', you can specify 'Any' if appropriate or you can even upload individual .swfs targeted for specific screen sizes.

If your code employs "liquid-layout" techniques, you could specify Stage.scaleMode = "noScale" in your code and then resize and scale elements yourself. 

In any case, it is a good idea to capture Stage.onResize events and readjust your layout and content accordingly.