My Catalogue provides the ability to add your own product codes for products or services. You could use those codes to adding surcharges such as delivery charges, and you can set a pricing type to automatically calculate the price based on a percentage of the order value (for example).
This video shows how to add a product which calculates a percent of the order total (after discounts) using the example of a delivery surcharge.
Further reading
My Catalogue Special Priced Products