To filter products on the warehouse you need to navigate to System>Shipping Methods>Webshopapps Product Matrix Rates>Advanced Settings and set the “Attribute to Filter Products On” to “warehouse”
By default this is set to “package_id”.
You will then need to take a note of the warehouse ID from the Warehouse Manager Screen.
In my example i have created 2 warehouses.
The next step is to configure the CSV file to change the Shipping Group column with the warehouse ID.
The CSV will look like this if you have 2 warehouse.
The next step is to assign the warehouse to the product:
When the shipping is calculated it will now use the warehouse id to match on.