When you create a product using the frontend “Add your listing” form, you set the destination automatically and once the product is approved, this destination gets added to Products > Destination.
Another way to add destination is by going to WP Dashboard 
Product ➡️ Destination.
The thing to note here is, theme displays cities or the 2nd level of destinations in the cards and search etc. So, ensure that you have assigned parent/child relationship for your destinations.