Hey, @eharrington5
You are correct! The default package size in Shopify is going to be used in all calculated shipping rates at checkout for your customers. In the case you have a variety of packaging sizing, I recommend using a third-party app to accomplish this. An app called Boxify will allow you to show rates that match how an order is actually shipped, whatever is in the cart, whatever the size of the box or boxes required. They also offer a 15-day free trial to see if it’s a good fit for our store!
I hope that helps. With that said, are you planning on setting up flat shipping costs or calculated shipping costs?