How to override Bootstrap theme files in sub-theme
You should put those files in yourtheme/templates/ (no sub-folder) and a quick cache clear after that.

See bootstrap_subtheme/templates/README.txt:


  This folder is where you should place all your overriding template files. By
  default, the Bootstrap base theme provides all the necessary template files in
  various folders inside of sites//themes/bootstrap/theme. For example, the
  page.tpl.php template file is located at
  sites//themes/bootstrap/theme/system/page.tpl.php. To override any of these
  files, copy them from the Bootstrap base theme and place them in here.