assuming you are referring to the main wppizza plugin (http://wordpress.org/plugins/wppizza/)
you might want to consider a multisite setup, though this depends on your exact requirements and any differences that might exist between the 2 shops

alternatively – if your 2 stores have *exactly* the same opening times, products etc etc – the following might be sufficient
https://docs.wp-pizza.com/developers/?section=delivery-by-post-zipcode