Hi, hope this helps you, as i had a lot of trouble too...
the .htaccess file needs to be in the folder that the index.php file is in
(i'm on a shared host, with an add-on domain, so mine was "home/public_html/mystore/"
and the htaccess file looks like this:
RewriteEngine On
RewriteCond %{SERVER_PORT} 80
RewriteRule ^(.*)$ https://www.mystore.com/$1 [R,L]