Technically, each piece of software may be unique in how you manage the preparation, upgrade/replacement of said item. JAMF and others are constantly working on "patch management' solutions, and you will find LOTs of threads here on jamfnaiton dedicated to sharing the best methods for updating individual pieces of software. Composer is a great tool (opinions vary) but it is what it is, but it is very manual. Check through the threads here for individual software titles and you will find all sorts of great solutions!
