:::note This tutorial assumes you're using Bukkit (or a fork of it, such as Spigot or Paper). :::
You'll first need to find the plugin you wish to install. Downloads can be found on a variety of sites. Common places are Spigot's Resource forums or the Bukkit Dev website. Make sure you trust the source of your downloads, as plugins have high-level access to your server.
In any case, save the plugin to your local machine. Plugins can either be uploaded via the web panel or through SFTP. If you're uploading in bulk, go with the latter.
In your server's root directory, locate the /plugins folder, if it's not there then create a new directory named /plugins. Navigate into this folder, and upload your plugin's file there! Most plugins will require you to restart your server before they take effect.