It depends. If you're coming from 4.1.2 ROM... and going to 4.3... Titanium Backup will have issues because they changed things on where/how files are stored in 4.3... but I think there is a fix for TB somewhere.
Never backup system data if you're updating to a new ROM. It messes things up. Just use the Backup new user apps & newer versions.
If you need help, check the FAQ first for whatever ROM you're on. Then ask questions.