Minor releases (i.e. 2016.x.y where "y" is the minor release number) contain bugfixes only and you SHOULD always update to the latest version.
Within a release series (e.g. 2016.x) we usually don't make backward incompatible changes of working code. This means you can upgrade within a release series to get the new features. Database changes will be applied by executing the "setup.php" script.
Contrary to stable releases, major releases that start a new release series (once a year in January) will contain incompatible code changes, cleanups and configuration changes. Thus, you need to adapt your application and the custom Aimeos extensions you've written.
More information about past, current and future releases is available on the roadmap page.
Because you copy the aimeos-settings.php and aimeos-routes.php files as well as the Twig templates to a local folder of your application and adapt them according to your needs, you must replace these files after upgrading the package to a new version (but not for minor releases).
If you don't use a version control system which can tell you the differences in the files, you should make a backup of your modified files first!
Copy the files using:
cp vendor/aimeos/aimeos-slim/src/aimeos-settings.php src/ cp vendor/aimeos/aimeos-slim/src/aimeos-routes.php src/ cp -r vendor/aimeos/aimeos-slim/templates/* templates/
Afterwards, you need to adapt at least the ./src/aimeos-settings.php file again because it contains the parameters for the database connection.