Hi @mehvishfatima01,
You can add Flipboxes Shortcode inside theme file using do_shortcode() function.
For example:
do_shortcode('[flipboxes id="8407"]');
replace id(“8407”) with your flipboxes shortcode id.
But the preferred way of using Flipboxes is Paste Flipboxes shortcode anywhere in any WordPress pages or posts.
For more details please check plugin Screenshots.
Thanks