There some updates in the articles in the Update Center that contain step-by-step information on how to upgrade existing versions of the software and apply patches on-the-fly. We've removed a step that mentions you that all program files should be closed before the patch or new version will be installed.
Our installation packages both for the communication server and messengers automatically close the program when the new version is being installed. So there are no needs to close, for example, the Management Console on the IM server or opened Message History in the clients.
You can review the upgrade procedure both in English and Russian.