How do I choose cross sells that are in stock or have inventory?

Unfortunately for now there's no filter for out-of-stock, or in-stock items inside our app. We know this is a source of pain for some of our customers which is why it's in our list of priorities to add it as quickly as possible. In the meantime, what we suggest customers to do, is to hide out-of-stock items from their collections by following these steps: https://help.shopify.com/manual/products/inventory/hide-out-of-stock