1. Stop your server.
2. Login to FTP or use the file manager.
3. Get bukkit or Spigot https://getbukkit.org/
4. Delete your old minecraft_server.jar file.
5. Upload the new jar file.
6. Rename the jar file to minecraft_server.jar (very important jar name is the same as before).
7. Start your server and you will see the plugins folder and other folders build.
17633 Gunn Hwy #145
Odessa, FL 33556