You then have two options that come to mind: You could just create a standard block using the Drupal UI, place the markup in the body of the block, and configure the block to "display on every page except" ...
<front>. Then assign the block to a region.
Alternatively, you can override tpl files in your subtheme and place the modal markup in those. You do this by placing a copy of the Bootstrap theme's
page.tpl.php in your subtheme. First create a copy of it called
page--front.tpl.php then add your modal markup to