Does this AJAX Shopping cart module work with up sell products in magento?

No, our extension doesn't work with the up-sells at the moment. However, it's possible to display related products in the ajax window boosts sales, as you offer matching items to a targeted buyer. This will help you to increase the average order value. To enable related products display, please navigate to System > Configuration > AJAX Cart > Selling Options and set “Display Related Products in Confirmation Dialog” to Yes.