Is there a way that I can just automatically set it to download the upgrades to the applications I use without getting the annoying notification signal every two seconds?
Annoyed me too, especially when the update after the update wouldn't update, but kept telling me there an update. Solution? DELETE
Whenever strange things happen in AppWorld/MyWorld I find that a quick reset (of MyWorld) will usually solve most problems.
Login to MyWorld, press & hold ALT and type R S T to reset. It will exit AppWorld and you can re open it and login again.