Updates to the template are extremely rare, almost all the updates happen on the framework level itself which takes care of any issues or updates. A framework update won't effect core css files, logo, footer, etc. Those all stay in tact.
All of our documentation is found here:https://www.shape5.com/documentation/
You'll find tutorials for changing the logo, footer, etc. The favicon.ico you simply over-write in the template's root folder with your own. If you have any specific questions please post in the Design Control board and we'll be happy to assist you from there.