In the custom masterpage add a css reference like below in the <head>
tag after the corev15.css is loaded :
<link rel="stylesheet" type="text/css" href="path/bootstrap.min.css">
If you want to ensure that your css is loaded after SharePoint's css is loaded, use it like below in the <head>
tag:
<SharePoint:CssRegistration runat="server" ID="customcss1" Name="path/bootstrap.min.css" After="corev15.css" />
Also, the bootstrap js file should be loaded at the bottom of masterpage to ensure page speed, just above the </body>
tag like below:
<script type='text/javascript' src="path/bootstrap.min.js"></script>