Minecraft → Settings is an editor for server.properties, so you don't have to edit the file by hand.
- Open your server in the panel and go to Minecraft → Settings.
- Change what you need. The ones people change most are difficulty, game mode, PvP, max players, view distance, spawn protection and the MOTD.
- Save, then restart the server. The file is only read when the server starts.
You can set the server icon on the same page. It's the picture players see in their server list.
Leave these alone
server-port and server-ip are set by the panel. Change them and nobody will be able to connect.
Making it private
Turn on the whitelist, then add people from Minecraft → Players. See manage players.