The way your phone is set up settings-wise is usually restored if you opt to restore from a backup that is normally created by iTunes before you upgrade/restore.
Well aren't you updating? You'd have to create the backup, do the upgrade, then do the jailbreak. Like I said though if you want to backup your jb stuff and you don't want to do it manually, you can use aptbackup or pkgbackup. Aptbackup is free but it isn't exactly always reliable. Pkgbackup is paid but more reliable.