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 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.