The best way to handle this order is to use the Dropship File Selection Rule to be use warehouse defined at product level. You can set this value by navigating to Administration -> Settings -> Shipping Tab. Select the “Use warehouse defined at product level” option for the dropship file selection rule if it is not already selected. Be sure that the products in the order are assigned to the appropriate warehouse.
Select the checkbox for the order and click the export to warehouse button from the Paid - Ready to Ship screen, you will select the warehouse you want to export the first line item in the order to. Repeat this step again for the next line item in the order.
If you are importing fulfillment data back from the warehouse, be sure that the ecomdash item ID is being sent in the sales order export so that ecomdash will make a match with the specific line item of the order so that the correct tracking is applied.