The ''HTML Head'' is changed slightly from the website version
<code>
<meta charset="<$mt:PublishCharset$>">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->
<meta name="generator" content="<$mt:ProductName version="1"$>" />
<!-- Bootstrap core CSS -->
<link href="<$mt:WebsiteURL$>css/bootstrap.min.css" rel="stylesheet">
<!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
<!--[if lt IE 9]>
 <script src="<$mt:WebsiteURL$>js/html5shiv.js"></script>
 <script src="<$mt:WebsiteURL$>js/respond.min.js"></script>
<![endif]-->
<link rel="start" href="<$mt:BlogURL encode_html="1"$>" title="Home" />
<link rel="stylesheet" href="<$mt:Link template="styles"$>" type="text/css" />
<link rel="alternate" type="application/atom+xml" title="Recent Entries" href="<$mt:Link template="feed_recent"$>" />
<script type="text/javascript" src="<$mt:Link template="javascript"$>"></script>
<!-- Open Graph Protocol -->
<meta property="og:type" content="article">
<meta property="og:locale" content="<$mt:BlogLanguage setvar="blog_lang"$><$mt:Var name="blog_lang"$>">
<meta property="og:title" content="<$mt:BlogName encode_html="1"$>">
<meta property="og:url" content="<$mt:BlogURL encode_html="1"$>">
<mt:If tag="BlogDescription"><meta property="og:description" content="<$mt:BlogDescription remove_html="1" encode_html="1"$>"></mt:If>
<meta property="og:site_name" content="<$mt:BlogName encode_html="1"$>">

<$mt:CCLicenseRDF$>
<$mt:CanonicalLink$>
<$mt:StatsSnippet$>
</code>

In the ''Entry Summary'' I just re-indented the code
<code>
<$mt:EntryTrackbackData$>
<div id="entry-<$mt:EntryID$>" class="entry-asset asset hentry">
 <div class="asset-header">
  <h2 class="asset-name entry-title"><a href="<$mt:EntryPermalink$>" rel="bookmark"><$mt:EntryTitle$></a></h2>
  <div class="asset-meta">
   <span class="byline">
<mt:If tag="EntryAuthorDisplayName">
    By <span class="vcard author"><$mt:EntryAuthorLink show_hcard="1"$></span> on <abbr class="published" title="<$mt:EntryDate format_name="iso8601"$>"><$mt:EntryDate format="%x %X"$></abbr>
<mt:Else>
    <abbr class="published" title="<$mt:EntryDate format_name="iso8601"$>"><$mt:EntryDate format="%x %X"$></abbr>
</mt:If>
   </span>
<mt:Unless name="hide_counts" eq="1">
 <mt:IfCommentsActive><span class="separator">|</span> <a href="<$mt:EntryPermalink$>#comments"><$mt:EntryCommentCount singular="1 Comment" plural="# Comments" none="No Comments"$></a></mt:IfCommentsActive>
 <mt:IfPingsActive><span class="separator">|</span> <a href="<$mt:EntryPermalink$>#trackbacks"><$mt:EntryTrackbackCount singular="1 TrackBack" plural="# TrackBacks" none="No TrackBacks"$></a></mt:IfPingsActive>
</mt:Unless>
  </div>
 </div>
 <div class="asset-content entry-content">
<mt:If tag="EntryBody">
  <div class="asset-body">
   <$mt:EntryBody$>
  </div>
</mt:If>
<mt:If name="entry_archive">
 <mt:EntryIfTagged>
  <div class="entry-tags">
   <h4>Tags<span class="delimiter">:</span></h4>
   <ul>
    <li><mt:EntryTags glue='<span class="delimiter">,</span></li> <li>'><a href="javascript:void(0)" onclick="location.href='<$mt:TagSearchLink encode_js="1"$>';return false;" rel="tag"><$mt:TagName$></a></mt:EntryTags></li>
   </ul>
  </div>
 </mt:EntryIfTagged>
</mt:If>
<mt:If tag="EntryMore" convert_breaks="0">
  <div class="asset-more-link">
   Continue reading <a href="<$mt:EntryPermalink$>#more" rel="bookmark"><$mt:EntryTitle$></a>.
  </div>
</mt:If>
 </div>
 <div class="asset-footer"></div>
</div>
</code>

In the ''Banner Footer'' add this
<code>
<footer class="footer">
 <div class="widget-powered widget">
  <div class="widget-content">
Powered by <a href="http://www.movabletype.org/"><$MTProductName$></a> | Layout in <a href="http://getbootstrap.com/">Bootstrap 3</a>
  </div>
 </div>
  <mt:BlogIfCCLicense>
 <div class="widget-creative-commons widget">
  <div class="widget-content">
   This blog is licensed under a <a href="<$mt:BlogCCLicenseURL$>">Creative Commons License</a>.
  </div>
 </div>
</mt:BlogIfCCLicense>
</footer>
</code>


Just before the closing body tag, add all the Javascript calls
<code>
<!-- Bootstrap core JavaScript
================================================== -->
<!-- Placed at the end of the document so the pages load faster -->
<$mt:Include module="Bootstrap Javascript"$>
</body>
</html>
</code>