To upgrade to a newer version, wipe the old program directory and install the new fresh version using the platform specific bundle. All settings are preserved since they are stored in a private place (or in case of instrumentation, on the servers).
The replacement update should be necessary only if some major library update had been included. Normally, you can happily use the Admin4 builtin online or manual update function.
Starting with 2.1.4, Admin4 includes an updater which installs updates or additional modules, if you have write access to the program module directory.
When clicking the "check now" button, Admin4 will retrieve information about available updates from admin4.org. These informations are cryptographically signed using admin4.org public key, and is checked against it locally.
If an update is available, you can press "Ok". Admin4 will start downloading the update from the download site, check its integrity using the SHA1 key, and replace all modules with the new ones. Restart the application, and you're up-to-date.
The manual updater lets you specify a directory or a zip file that is used for upgrading. Some name conventions apply: Admin4-xxx used for core/complete updates, modXX-yyy for installation/update of single modules. Select the directory or the zip, and hit "Ok".