If all goes well, your apps should still be there after you upgrade (providing you don't brick your phone =P) so all you need to do is use them again and set the permissions.
hey all, Did my first upgrade today and lost all my apps. Nothing there at all, did my backup once so still have my contacts but even lost my browser until I did a hard reset and got that back. Lost all pre-installed pics and games, anything I can do??