Frontend template extensions that take over a large part of the template rendering can sometimes be confusing. If you understand the rendered page template as the end product that's generated by the CMS, but not a part of the CMS's functionality, everything will become easier and more transparent (less black boxes).
My advice would be: don't use a framework extension, get bootstrap from github, ideally in the LESS version - use one of the many lessphp extensions to parse less while developing - and create your template in whichever templating system you're comfortable with.