Here Google Webmaster Tools (GWT) states that you should verify each significant section of your site and if you have  http:// and https:// versions, you should add each as a separate site.
You cannot submit a file to GWT like it has to be a folder (doesn’t that potentially create some canonicalisation issues?)
Webmaster Tools data and reporting work best on a site level. For example, if your site has separate sections for different countries, we recommend adding each of those subsites or subfolders as a separate site. For example, if you have a travel site with specific subfolders covering Ireland, France, and Spain, you could add the following sites to your Webmaster Tools account:


As soon as you add a new site GWT wants a sitemap also – why submit a sitemap
Then Google also suggests looking at their Search Engine optimisation guide click here for the PDF doc as at Oct 2013.
Also if Google cannot find your Robots.txt file it might suspend crawling your site, so make sure you have a Robots.txt even if it just contains the allow  all line
User-agent: *

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