In your control panel, click on the server you want to install plugins on, then go to Files that is on the left sidebar. Click on the plugins folder and this is where you upload .jar files of plugins.
As an example, if I wanted to install the World Edit, I would drop a file named something like World-Edit.jar into the plugins folder.
Once you've added a plugin, reload(not recommended) or restart the server in order for the plugin to generate it's folder in the plugins folder. The folder it will generate is where you can configure the plugin, if needed.