Today I had time to install Cumulative Update 2 (CU2) for ConfigMgr 2012 R2. KB2970177 (CU2) solves a lot of issues in ConfigMgr and is therefore highly recommended. More about CU2 improvements in another blogpost. No need to install CU1 anymore, because it's integrated in CU2 (which is same as other cumulative update packs before). No need to install the latest Endpoint Protection anti-malware platform update also (which is from March 2014 at the moment). This one is integrated in KB2970177 (CU2) as well.
After installation, which is default as always, there will be update packages created and the version will be updated (5.0.7958.1303). To be better safe then sorry do a restart of the ConfigMgr server after patching. Still strange that Microsoft is saying it isn't needed (TechNet), but the installation wizard mentions it is needed! :)
After setup you have the benefit of all updates and hotfixes. Don't forget to update other ConfigMgr servers, consoles and clients as well. You can find packages for that in the console after the update.