If you want to just change your /server command colors, I'd suggest you to edit messages.properties in BungeeCord.jar, if you open it with WinRar software you can find it there.
Tried it. That doesn`t change the actual servers. It`s in the cmd_server.jar I just don`t know how to edit it to make it a different color.
In order to change servers name you'll need to edit cmd_server.jar, either decompile it or find it from bungeecord's github.