After you have received your custom URLs from StackMaps, edit the theme.config.php file located in your custom theme (/usr/local/vufind2/themes/YOURLOCALTHEME/). You will need to add some entries to the 'js' and 'css' sections as shown below. If you already have entries in these parts of the config, add these alongside the existing ones. If you do not have 'js' or 'css' sections yet, you should create them.

<?php
return array(
    'extends' => 'bootstrap3',
    'js' => [
        'https://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js',
        'https://www.stackmap.com/integration/YOURINSTITUTION/StackMap.js',
    ],
    'css' => array(
	    'https://www.stackmap.com/integration/YOURINSTITUTION/StackMap.css',
    ),
 );

If you encounter problems in the display, contact support@stackmaps.com