Orders are normally process by Spark Shipping after they are marked as Paid.
In the case of Purchase Orders, they are paid after the order has been received.
In Site -> Advanced Options there is the option:
Send Shopify Purchase Orders upon creation
Once this enabled, for Shopify orders using 'Purchase Order' as the payment gateway, these orders will be imported into Spark Shipping and processed while still in a payment pending status.
This will only apply for orders received through the Purchase Order gateway. All other orders will be process as usual.