We recently had to upgrade the OS on several BlackBerry Storms for some customers. They are using BlackBerry Professional Software (BPS, the now discontinued little sister of the BES).
You cannot push the software to the user if you are using BPS
The easiest way to do this is to:
-Install BB desktop manager on the user's machine
-Go to http://www.vzam.net/blackberry/ and download the latest OS (choose corporate email)
-Connect the device to the machine
-Navigate to the Application Loader
-Choose Update Software and Start
From start to finish the update takes about an hour.