[eluser]Mavarik[/eluser]
[quote author="InsiteFX" date="1399387820"]You need to include the required bootstrap files in your php view files, I usually create a header view for that.
Then just create bootstrap files in your views folder and add the header view to them.
If you get stuck I can create a sample project for you latter this week.
[/quote]
This maybe not the best practice, but is working for me on a couple BS2/3 themes.
I have header template - which includes code until just before </head> tag.
Then Nav and Footer templates.
Then in the content pages I do something like this.
$this->load->view('templates/header', $this->data);
<!-- Put extra header tags in here css/js etc -->
</head>
<body>
$this->load->view('templates/nav', $this->data);
<div class="main-content">
rest of page content here.