Restore Backup after Jailbreak

Hi guys,

I have freshly jailbroken my PS3 Slim and want to restore a backup I made before the jailbreak via the backup utility.

- When I made the backup I had the latest Original Firmware 4.31 installed
- Then I downgraded the PS3 to 3.55 and upgraded to the CFW 4.25
- Now I want to restore the backup, so that all my settings, videos, pictures etc., my downloaded PSN games and most importantly my save games are restored.

Now my questions:
Can I restore the backup normally via the backup utility without messing with my CFW?
Will I lose the currently installed apps (Multiman, Toggle QA) if I restore the backup or is there a way to restore the backup without formatting the HDD?

I already searched the forums but didn't find an answer to this specific problem. Hope somebody can help.