This couldn't be easier. In the Import Settings screen, simply specify whether existing products should be updated with data in the import file. You can also choose to delete existing products that are not in the import file.
Start by using WP All Export's Bundle option to export the products from the source store. During the import to the target store, WP All Import automatically recognizes the instructions contained in the Bundle file. This lets you migrate WooCommerce products with just a few clicks.