Lauri,
I feel your pain. I just had to go through this exercise a couple of weeks ago when I upgraded my RSView ME dev package to 3.2, but still had terminals out there with Firmware version 3.1.
I liked the Compact Flash method for upgrading. Pretty straight forward. You just have to remember 2 important things:
1. BEFORE upgrading, make sure to go into the config screens on the terminal and disable the autostart feature for your application. If you don't, you'll be in a world of hurt since the upgrade wipes out your communications configuration and your app will lockup because it can't talk to your PLC.
2. Remember to reconfigure your communications on the terminal(e.g. IP address on Ethernet terminals) AFTER upgrading and before restarting your app or you will find yourself again in a lot of pain.
Failing to follow these two steps will result in having to basically wipe out your runtime file from the terminal and then reload it after you have correctly configured communications.
Use the FUW utility to make your compact flash card and remember that as soon as you insert it into the slot on the terminal, the upgrade process initializes.
Good Luck,
Jeff