If you want to update Shopware itself, then there are 2 basic options.
If you are a plugin manufacturer, you could simply switch to a new dockware Shopware version and upload your plugin again. That should be fine.
If you have full projects, then you might either want to update Shopware using composer or through the built-in Shopware updater tool. Afterwards make sure you download the source again to your host to keep it consistent.