Most CCM 5 upgrades are a single file that is uploaded to the server via FTP or from the DVD drive. It is a simple process. The upgrade actually is loaded on a seperate partition.
You tell it where the file is, it uploads it, gives you a checksum to compare to the Cisco checksum and then you tell it to install and reboot to new partition or to stay on the active partition until you are ready. I did it once with an active call up and it didn't affect the active call at all. Until the reboot of course.