Basically register account, enter your domain, update your DNS records with an A (replacing the Github pages IP) and TXT record (for verification).
While the change in DNS was in couple minutes on Gandi, Kloudsec DNS took an hour or two to register the change. After that, you go in the "Security plugin" and enable it. If you're using an apex domain, you can remove the www. HTTPS request, since you won't get the cert for that (if you do have an apex domain then you probably know about the CNAME trick on Pages, unless your DNS provider supports ANAME or ALIAS records for the apex domain - Gandi doesn't). It took couple hours again to get the cert.
When it's done click on the "Settings" cog icon for the desired HTTPS domain and enable HTTP-> HTTPS redirect and HTTPS rewrite, then you're set.