We are shipping wine. There are common package sizes, 3 bottle, 6 bottle and 12 bottle boxes made to carry wine. The shipping calculator does not take into account the size of the item in the cart, only the weight. How can we use Shopify to make this work? It's not like we can jam 18 bottles into a 12 bottle box... (which is currently what is happening in the "calculated shipping")
Which carrier you are using?
If you are shipping via FedEx, try the FedEx Rates, Labels & Tracking app which will help you with the packing process. With the Box packing feature in the app, you can automatically pack the bottles into the available FedEx boxes or custom boxes based on the dimensions of the product which can be configured within the app.
Also, you can display real time FedEx rates, print labels and also handle FedEx tracking with the app.
Rather than going with dimensions and weight, I can suggest you a better solution. What if you can define specific boxes and in each of those boxes you can decide how many of those bottles shall go : 3,6 or 12? According to me, this should be the simplest solution. You can try this with the Multi Carrier Shipping label app.