For wholesale, we ship and then send the customer an invoice - I believe this would be relatively common scenario for many Shopify stores.
Ideally, we would be able to enter an order in 'Drafts', have that order show up in our shipping app (Shipstation) and then generate an invoice using something like Shopify's 'Order Printer'. However, unless the Draft order is fully paid for, Shopify doesn't push the order over to Shipstation (we don't want to have to re-enter the entire order twice in two different systems). While we could mark these orders as 'paid' in order to have them pushed over to Shipstation, that would obviously make it harder to keep track of who has paid and who hasn't.
With Shopify POS, a partially paid order (even $0 paid) will be pushed over to Shipstation (as long as you enter Shipping address); the problem here is that Shopify POS doesn't allow for adding a shipping charge (you can add a Custom sale, but this complicates accounting, doesn't integrate nicely with shipping apps, shows up as a line item on foreign custom forms, etc). Not to mention the need to bring out the iPad...
It seems like all the pieces are here to make this work, but just not properly integrated.
I've been in touch with Shopify about this - what I would consider a bug - but curious if anyone out there has figured out a clean solution working with the current limitations.