A simple way would be to use Bootstrap CDN. For CSS, simply include this line in the <head> section of every webpage (somewhere in your view files, depending on how you have structured them):
<link href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css" rel="stylesheet">
Bootstrap's plugins depend on jQuery, so you'll need to include jQuery before Bootstrap's JavaScript:
<script src="//ajax.googleapis.com/ajax/libs/jquery/1.11.0/jquery.min.js"></script>
<script src="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js"></script>
Simple example page:
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<title>Your great site!</title>
<link href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css" rel="stylesheet">
</head>
<body>
<div class="jumbotron">
<div class="container">
<h1>Hello, world!</h1>
</div>
</div>
<script src="//ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>
<script src="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js"></script>
</body>
</html>
Alternatively you could host the files on your web server. Upload the relevant files to a publicly accessible directory. I'm going to assume that they are in an assets folder, in your web root, like this:
+-- public_html
| +-- index.php
| +-- assets
| | +-- css
| | | +-- boostrap.css
| | +-- js
| | | +-- bootstrap.js
| | | +-- jquery.js
| (other files/directories...)
To include them in your view files, you can link them like this:
<link rel="stylesheet" href="<?php echo base_url("assets/css/bootstrap.css"); ?>">
<script type="text/javascript" src="<?php echo base_url("assets/js/jquery.js"); ?>"></script>
<script type="text/javascript" src="<?php echo base_url("assets/js/bootstrap.js"); ?>"></script>
You'll need to have loaded the URL Helper to use the base_url() function.