Depends on what you're backing up. Making a copy of the SD card contents will archive everything, but the flash does not wipe that stuff anyway.
Flashing the ROM will essentially "factory reset" your phone and wipe off contacts, calendar, text messages, etc.
If you want to keep any of that stuff, thats what you need to back up. If your contacts are all phone contacts, export them to your SD card. You can then import them back in once you're done.