Run the backup before you install the ROM, then once the ROM is installed (with its shiny new shutdown screen), just run the restore process.
The back up and restore can take some time, but seem to work. At least I still have my custom theme, and most of (if not all) my applications in place, and it has happily resynchronised with Outlook.
One thing to note - the update restores an SPV to its original application-locked state, so if you've unlocked it in the past, you'll need to do it again. Of course, I'd always recommend unlocking your SPV so you can run all the available applications.
Just pop along to this page of unlock instructions on coolsmartphone.com and follow the directions. If you use the download method, you'll need to sign up as a site member...