Elive has an own, fully automated and totally light updater tool, you may have noticed it to update recently with the multiple-screens features
The tool was designed to be automated specially for important things (automated fixes if needed) and also includes a full upgrade more delayed (monthly or weekly), which asks you to upgrade the full system
In short, you dont need to care about anything
As about own installed packages, there's a feature in the installer to maintain them installed among upgrades (as a list that you can modify yourself)