Apliiq Warehouse orders do not use the same shipping profile as Apliiq Print On Demand orders.
How you are charged for shipping your warehouse orders
Apliiq Warehouse shipping rates are set based on where your products are being stored and where your orders are being shipped to. Depending on the distance between the origin and the destination, a zone is assigned, and based on the zone a rate is set. The Apliiq Shopify app will charge you based on the exact zip codes of the Apliiq factory and your customer's destination address.
Shipping Zones for storing product in Los Angeles factory

Shipping Zones For storing product in Philadelphia factory
How to charge shipping for your products in your store
You have 2 ways to charge your customers for shipping of your products.
1. The Apliiq Shopify app will create a Shipping profile that sets a shipping rate for each state. The rate will be very close to the shipping rates you are charged by Apliiq, but they won't be identical.
2. Setup carrier calculated shipping directly within Shopify. This is currently a paid feature offered by Shopify.