Hello,
Your current need typically fit the HikaShop Warehouse system, I will guide you to better understand its principle.
1. From Main HikaShop Configuration, go to System dropdown => Warehouse
2. Click on New button to create a New warehouse (or several if required)
3. From this, in your Shipping method, Restrictions part you can now restrict Shipping Methods from Warehouse
4. Go in your product backend, in Restrictions and Dimensions part associate your product to the required Warehouse.
Result, if everything is correctly set, if a customer add in his cart 2 products from 2 differents Warehouse (and so different 2 Shipping method), both shipping method will be used to calculate order shipping price.
Hope this will help you to manage this case and fit your needs.
Regards