Best practices for applying SOA-P 5.3.1 2014 roll-up patch 1

Issue

• In the readme file of the the patch file BZ-1073034.zip of Roll up patch SOA_5.3.1_1_2014 [1] , there is a list of many files in .jar format. And some in the following .xml, .java, .class, .properties, .sql etc formats as well. Do the users need to replace them all in one go?
• It seems there are a lot of such files to patch or replace in one go. So can users just patch one type of files first, like .jar and then do another batch on the next day and so on and so forth?
• Is there a link for best practice for doing patching like this one or in general?

[1] Roll up patch SOA_5.3.1_1_2014