If you have an SSL certificate installed and configured properly for your webserver, and want to have FunnelFlux exclusively use the HTTPS protocol, you can go to the system settings page of FunnelFlux and turn on "force HTTPS".
Be sure to test your tracker and links before making this change by loading via http and https, i.e. confirm the SSL is working before turning this on.
Not doing so may result in breaking of tracking links and your own login.
If you have SSL installed and configured correctly, the https links should work fine without an changes.