You can add all the following pages to Google webmaster tool :
http://www.mysite.com/fr/
http://www.mysite.com
You can add all URLs in same sitemap as you know that sitemap can have 50k urls.
You can have 301 or canonical tag if you have duplicate issues
Yes you should use hreflang for each url
If both urls have same content but one in english and another one in french then absolutely there would be duplicate issue.
Please follow this step
Go to admin area Open Menu Preferences > SEO & URLs And then edit index.php from the page list (url lists) On next interface you will see input field for title, keyword and description metatag