Hi Joseph,
The Sendly app might be able to help you. You can choose to have free shipping on select SKUs. You can leave all the other shipments in your system and Sendly will figure out those cost, based on the weight provided, through a variety of carriers.
Sendly is free to all Shopify users and it’s currently in Beta. You can find it here: http://apps.shopify.com/sendly
Feel free to contact us if you have any questions – support@secureship.ca.
Cheers!