During the Checkout process in Magento a customer can select "Checkout with Multiple Addresses"
This allows the customer to specify a different shipping address for every product on the order
You can the specify different Shipping Methods for Each product. Flate Rate, Overnight, 2-Day, etc
Once the order has been completed you will see that 2 orders have been created through one checkout process
You will then see in the Magento Admin these 2 orders
Since a split shipment during checkout in Magento generates separate orders, each with their own shipping address, tax rate, shipping charges, etc....these orders will be imported into CounterPoint the exact same way as if the 2 orders were placed separately.