One of the most anticipated changes in iOS 5 is the way that notifications are handled. The Notifications Center is certainly an improvement on how notifications were displayed in previous versions of iOS, and with a little bit of time and thought can be fine-tuned to suit your priorities and preferences.
To do so, open the Settings app and double-tap on Notifications. On the next page you will find a list of all apps that can be configured to appear in the Notifications Center. You can choose to have these displayed in the Notifications Center either chronologically or in your desired order. If you select the manual sort option, double-tap on the 'Edit' button in the top right of the page and then drag and drop apps into your preferred order.
You can control how notifications are handled for each app by double-tapping on its name in the list. You can decide whether it appears in the Notification Center, how many updates to show if it does, what type of on-screen alert you would like, whether or not the numbered update badge is shown on the app’s icon, and if its notifications should be displayed on the Lock Screen.
It might take some time to get things exactly as you want them, but it is certainly worth it.