You need for this tutorial:
A custom jar, I have chosen "Bungeecord.jar" from http://ci.md-5.net/job/BungeeCord/
Warning: making a reinstallation will delete all of your data (maps, plugins etc...), so make a backup before in "Maintenance" panel with the "BACKUP NOW" button.
1. Go to download "BungeeCord.jar".
2. Go to "Maintenance" panel.
3. Click on "REINSTALL" button to open the list of all packs.
4. Choose "OPENMOD" pack for installation.
5. Click on "Openmod" pack.
6. And "CONFIRM" for installation
7. Wait during the process.
8. Go to "FTP" panel to see if your server is empty for the becoming new custom jar. If you have always files try again Openmod pack installation.
9. Here, you can see there is nothing in the disk, this means that the installation was successful to put the new jar.
10. Open Filezilla and connect with your FTP CREDIENTIALS into your server disk.
11. Select the downloaded "BungeeCord.jar" file from your computer and drop to Filezilla into your server root.
12. Go to "Settings" panel.
13. Click on "SERVER VERSION" case to open all versions, select in --Uploaded on FTP--"BungeeCord" pack.
14. Click on "SAVE CHANGES".
15. START Server with play button.
16. Go to "Console" panel, to see if the server has started successfully.
Everything is ok, you can enjoy your new custom pack.
If you want to configure BungeeCord servers please watch this tutorial :
You can see how to add the lobby server, game servers, and everything you need to create linked servers.
Updated version of the tutorial: How to use BungeeCord 1.11