Problem with submenus
Create such sub-theme folder manually. The folder name you'd use for it will be the machine name of your subtheme.

For more details, refer to:


"Creating a sub-theme" (= Community documentation that applies to any sub-theme).
"Sub-theming" (= documentation about sub-theming specific to Drupal's Bootstrap theme).


If you prefer to look at a great (I think) example of a (contributed) Bootstrap sub-theme, then have a look at the Bootstrap Business theme.