If you mean replacing a cart that has already been implemented by another software, you would want to basically remove all the add to cart buttons generated by the other cart. Then you would want to replace those add to cart buttons with the ones generated by eCart and then generated the eCart display manager on a cart page. And then run through the eCart Wizard to set up the checkout pages.
If you mean replace a cart that is generated by eCart, you would just apply the display manager to a different page and modify the add to cart buttons to point to that page.