Yes, you can! JoeLister supports Merchant Fulfilled items. Use the pulldown filter in your Amazon Inventory tab to toggle between AFN (Amazon fulfilled) and MFN (Merchant fulfilled) inventory (see the screenshot below).
The listing process is the same for both AFN and MFN items. However, when an MFN item sells you'll receive email confirmation that the item has sold. Then, you must fulfill the item on your own, as JoeLister can not fulfill MFN items for you. You must also upload your own tracking information to eBay once it is obtained and available.