Updating plugins can be relatively simple depending on the plugin.
In most cases, updating a plugin only requires you to download the new plugin's .jar file from https://www.spigotmc.org/resources/categories/bukkit.4/ or https://dev.bukkit.org/bukkit-plugins/ and replacing the one in your plugins folder then restarting the server.
In some cases the server should be offline before doing so (in general we would advise this whenever updating plugins) as some plugins actively load from the jars so if the jar is changed while the server is running it can caue that plugins features to stop working/play up.
However, some new versions of plugins have updated configs also, which means you either have to delete the config files for that plugin in addition to replacing the .jar file for the plugin, or add the new config sections manually. Usually the config files for plugins are in the plugins directory in the folder with the name of the plugin and are usually named "config.yml" or something similar. Some plugins have multiple config files, so you may need to delete them also. Instead of deleting the config files, you can also rename them just in case you need to revert back.
When updating your plugins always make sure to check the changelog for any additional information regarding whether the configs have changed or need deleting.