Can you please confirm the exact version of BES 5.0 that you are running (e.g. 22.214.171.124)? Also are you saying that you can't get past step 1 which is to install the firmware onto the BES?
Step By Step Guide:
Permitting users to update the BlackBerry Device Software using the BlackBerry Web Desktop Manager - Update Guide - BlackBerry Device Software - 5.0.2