Using Store Commander's CSV import tool, you can update stocks on products/combinations in specific warehouses.
In your CSV file, you'll need to add a quantity column per warehouse, as shown on the screenshot below:
The corresponding mapping will then be as follow:
Note that there are 3 'quantity' fields you can use:
Note that if the product or the combination is not associated to any warehouse, the import process will automatically associate to the warehouse specified in your mapping option.