The best solution is to clone the controls in code and update the module definition within Kentico to point to those new code files.
Start with the
/CMS/CMSModules/Ecommerce/Controls/UI/OrderList.ascx control. Clone this to your custom folder and make sure you modify the namespace and class name, if you don't you'll get build errors. From there, start making modifications to the code. Lastly, go to the Modules application and look for Ecommerce, then go to the User Interface tab and find the Orders node and modify the URL of the page (not user control) the orders link will load. This will require you to clone the
/CMSModules/Ecommerce/Pages/Tools/Orders/Order_Listing.aspx page to your custom folder. Make sure you modify the control reference, namespace and class name in that page too.