Hi,
Your Main Joomla template would load the Bootstrap stuff wouldn't it?
For my custom Joomla template I did this:
// Add JavaScript Frameworks
// JHtml::_('bootstrap.framework');
unset($this->_scripts[JURI::root(true).'/media/jui/js/bootstrap.js']); // stop Joomla loading bs2.js
unset($this->_scripts[JURI::root(true).'/media/jui/js/bootstrap.min.js']); // stop Joomla loading bs2.js
unset($doc->_scripts[$this->baseurl.'/media/jui/js/bootstrap.min.js']);
unset($this->_scripts[JURI::root(true).'/media/system/js/modal.js']); // stop Joomla loading bs2 modal.js
unset($this->_style[JURI::root(true).'/media/system/css/modal.css']); // stop Joomla loading bs2 modal.css
$doc->addScript('templates/' .$this->template. '/js/bootstrap.min.js');
$doc->addScript('templates/' .$this->template. '/js/headroom.js');
$doc->addScript('templates/' .$this->template. '/js/multiselect-bs3.js');
$doc->addScript('templates/' .$this->template. '/js/template.js');
// Add Stylesheets
$doc->addStyleSheet('templates/'.$this->template.'/css/template.css');
<br>
I stopped Joomla! from loading the Bootstrap 2 stuff, and load Bootstrap 3 stuff and other bits instead.
NOTE: If using Seblod to output forms and lists etc all is good, however, if you use something like Featured Articles, then Joomla will STILL load some BS2 stuff. My modals wouldn't work.