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:
quantity: the current stock is replaced by the value specified in the CSV file
quantity - add: the value specified in the CSV file is added to the current stock
quantity - remove: the value specified in the CSV file is substracted from the current stock
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.