[ame=http://www.youtube.com/watch?v=pbPep5d1tog]YouTube - STOP Alerts From Popping Up On iPhone, iPod Touch, And iPad - iOS Vlog 337[/ame]
AlertBlocker is a tweak in Cydia that will allow you to turn off your pop up alerts the way you want. You can choose from several categories of push notifications that you receive in iOS. This being things like text message alerts, voicemail alerts, etc. The tweak works pretty well if you have a use for it, go grab it. AlertBlocker is $.99 in the Cydia store.