I've been always been restoring my backup since my Original iPhone (I still got my first ever SMS i sent form my iphone to my (EX) girlfriend at the time.
Now for Cydia App, i do installed them manually and once by one, making sure of compatibility, updates and settings. I test drive the app for a few hours (or a few days depending of what it is) before installing the next one. I know this is a LONG process, but this may be why I havent had a issue with my personal phone and I can keep restoring my backup over and over.