The template files present in a Product Enquiry Pro (PEP) plugin can be overridden easily by copying the template files to your theme or child theme.
To override the templates, copy the template file into a directory named /quoteup in your theme or child theme keeping the same file structure but removing the /templates/ subdirectory.
For example, if you want to override the template /product-enquiry-pro/templates/public/enquiry-mail/products-table-head.php, copy this template file to /your_theme_or_child_theme/quoteup/public/enquiry-mail/products-table-head.php location.
In the same way, if you want to override the template /product-enquiry-pro/templates/admin/pdf-quote/tax-shipping-note.php, copy this template file to /your_theme_or_child_theme/quoteup/admin/pdf-quote/tax-shipping-note.php location. You can find more about overriding the Tax and Shipping Note in Quote PDF here. Similarly, you can override any of the template files by simply copying the template file to your theme or child theme.