Not sure if these workarounds will be suitable for you, but here's what I've found: Orders that are pending payment in Shopify go to the "Awaiting Payment" section of Shipstation.  If you "Mark as Paid" in Shipstation they then get sent to "Awaiting ...

We are in need of the same functionality.  Whats the point of net terms if you can't fulfill the orders in the meantime?