Step 1. Go to Cydia and download "aptbackup"
Step 2. Open up aptback up from your springboard and press "backup"
Step 3. Connect your device to your computer and go to iTunes and right click on your device name and click backup.
Step 4. Let iTunes back up your device after this you can go ahead and update. When you re-jailbreak your device after updating just download "aptbackup" again from cydia and press restore and you should get all your apps back from cydia(including themes, ringtones games)