There's a <initialwindow> tag in the application descriptor file . It has a property to set <x> & <y> coordinates of the initial window created. See if it solves your purpose. http://livedocs.adobe.com/flex/3/html/help.html?content=File_formats_1.html
Unfortunately, as I mentioned, they only allow you to set specific x/y pixel values at design time, they dont let you center the window because at design time you do not know the size of the users screen.
You can keep the visible property of your initial window to false in the descriptor file. Once you are there in the code, check for the screen API (http://help.adobe.com/en_US/air/reference/html/flash/display/Screen.html) to get the visible bounds & try to position you app as you like. Once done you can set visible property back to true again. Let me know if that helps.