It is important to have Bootstrap as the first CSS link in your head tag, followed by any other CSS links. If you have all the Bootstrap CSS files in your css folder, that's a good practice.
To ensure proper order, place it at the top like so:
<head>
<title>Title</title>
<!-- Bootstrap core CSS -->
<link href="css/bootstrap.min.css" rel="stylesheet">
<!-- General CSS -->
<link href="css/general.css" rel="stylesheet">
<!-- Font Awesome CSS link -->
<link href="http://maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">
<!-- Javascript here -->
</head>
Consider using the bootstrap.css file for easier editing purposes as well.