Upgrading an EX controller is no different than any other controller, it's fairly simple on the newer platforms since 9.0.
Make sure you have active SWA, go into the Server Manager and download the update, then initiate the upgrade. My experience is this takes about 90-120 minutes per controller.
You can do it the "old" way with the MiVoice Business Software Installer, but this way is so much easier and takes less intervention. If you have remote access to any PC on the network you can do the upgrade remotely. I have done dozens of them without incident, not that things can't go wrong, but I haven't seen an upgrade fail in a very long time.