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air is for desktops. it should be able seemlessly get it to run in your stores from fb.
I haven't found a way to do from a single project, as each project *must* be targeted to either Web or Air.
Your main application window will have to be different, i.e. Application vs. WindowedApplication. But after that, apart from AIR specific stuff, you could share source between projects, e.g. all your components, actionscript etc.
Basically create two projects:
myAppWeb - Web app
myAppAir - Desktop app
Then using the Properties on both projects, you can point an additional source directory to code that is common between them both.
Or do what I do a lot of the time. Design and build as a web app. then just before deploy, create a new Air project, copy all the code over, add Air specific code then deploy.