To whitelist your server, simply log into the Control Panel, go to configuration files, then to serveradmincustom.xml. Within this file, you will have access to permissions, admin accounts and more.

This is very important:

If you even have one user whitelisted on your serve,r this means your server is whitelist only. You must add all players who will play to your serveradmincustom.xml file manually.

To do this, simply scroll down to your <whitelist> section. By default, it will look like this, To add someone to the whitelist, Add their steam ID and uncomment the following line, 

<whitelist>
        <!-- <whitelisted steamID="SteamID64" /> -->
</whitelist>

To whitelist multiple users, add whitelisted steam id's within the whitelist tag as shown:

<whitelist>
        <whitelisted steamID="SteamID64" />
        <whitelisted steamID="SteamID64" />
        <whitelisted steamID="SteamID64" />
</whitelist>

Alternatively, you can add yourself as a whitelisted user, then add users to whitelist via the following console command:

whitelist add <PlayerName> <PermissionLevel>

Like So:

whitelist add entangld 0

You may only this command via Telnet or the in-game F1 console.