To achieve this, you will have to use an app like the Multi Carrier Shipping Label app that helps you handle the packaging with the weight & dimensions of your products. You can add custom boxes based on the product dimensions and the app automatically chooses the right box based on the order. Also, the app helps you automate the shipping process.
Unfortunately, Shopify offers one standard box size to send off for all dimensions, resulting in incorrect rates from being charged at checkout. You will need a third-party shipping app to get the accuracy you're looking for. Intuitive Shipping will be a fantastic fit for your store to solve this. We have a few packing options that can help, and it sounds like setting all items to ship separately in your product settings within Intuitive Shipping is the way to go for you. You can connect with our team at firstname.lastname@example.org to learn more - the more detail, the better, so we can guide you properly :)
We are currently offering a Starter plan for new and/or lower-volume stores, you just have to connect with our team to have it manually adjusted for you. We're also free to install and offer a 14-day live trial, so try us out risk free :)
Please keep in mind that with all third-party shipping apps on Shopify, they require merchants to pay $20/mo for third-party calculated rates if you're on the Basic or Shopify plan. We've been trying to get them to remove this significant barrier, especially since our Starter plan costs less.