I don't understand the distinction or the pros/cons of the two options. Can anyone elaborate?
first of all I belive your title should read "Notification Center: Sort apps Manually or By Time?" you don't sort apps in iMessage
but to answer your concern you can choose whether apps in the notification center appear as they come so if you get a text that will show at the top, then say FB sends something that appears above your text and so on with each new notification.
OR
you can manually organize your notifications and say for example no matter waht notification comes in texts will be at the top then emails then FB then words with friends, or however you decide to organize it.
make sense?
I personally like organizing things myself, to make sure things like texts or missed calls are always at the top no matter what comes next. The con to this is that any other newer updates that you might be relying on from other apps will father down the list.