Yes, you can! JoeLister now supports Merchant Fulfilled items. Check out the pulldown in your Amazon Inventory page. Using this you will be able 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 get an email telling you that you've sold an item. You'll have to then fulfill this item on your own, as JoeLister can't fulfill your MFN items for you. You'll also have to upload your own tracking information to eBay when you have it available.