Google WMT feature to 'Add a site' asks users to enter a URL, and gives example 'www.example.com' - which is not helpful when trying to add an https site
To add the https version of the site, just look at the URL in WMT for http version and change it from https://www.google.com/webmasters/tools/dashboard?authuser=0&siteUrl=http://www.domain.com to https://www.google.com/webmasters/tools/dashboard?authuser=0&siteUrl=https://www.domain.com and you will be prompted to verify ownership
Also associate the new https account with your google analytics account - this will remove association with your http site, which seems a limitation on WMT/GA - they should fix that.
Also - remember to upload your disavow file to the new https account as well!