When placing popups, the Flex PopupManager class gives a great method called centerPopup. But please, don't use that. Rarely do you actually want a popup centered. It's often times much more visually pleasing to above there. I like placing the top of the popup around 20% of the height of the application.
A centered popup:
Of course this isn't a hard-set rule. Sometimes you want your popup in other locations. For instance, if it was triggered by a toolbar at the bottom of your application it makes no sense to force the user to mouse that far up.
Here's a quick method to place that popup, I register my main application component on startup, but you could easily pass that in or use a stage reference instead. This method won't work well if you popup is too tall.
public class PopupPositioner
public static var mainApp:UIComponent;
public static function centerPopUp(popup:UIComponent) : void
popup.x = mainApp.width / 2 - popup.width / 2;
popup.y = mainApp.height / 5;