There's Clover Configurator, it contains a tool for updating the clover installation, but I haven't tested that yet.
The manual way is:
Backup the config.plist file in the Clover directory, the kexts folder and drivers folder.
After that, search for updated versions of those kexts and drivers. Next verify if there's something that needs to be updated/removed/changed from the config.plist file. TIP: The clover installer can be used to update some drivers.
After that, just paste the backups in the new clover installation. If your kexts is in a version folder (like 10.10, 10.11), and you don't need to change any of them, just rename that folder to 10.12 or 10.12.4 (last update), or rename to "Other".