I moved on to ShipStation. I use them for one of my other stores. They have the flexibility I need to move the number of labels up or down depending on the needs of the item ordered. Pricing is similar though I believe Shopify holds an edge here. Bottom line I just got tired of performing work arounds on a problem that Shopify refuses to address.
I have further questions on this. I received 1 order that will take 4 boxes to fulfill. The customer paid 1 price for shipping. I am trying to do what you suggested with counting 1 box at a time as partially fulfilled and printing the shipping label. When I go back to fulfill the next box, it is saying to create shipping label and then buy shipping label. So, at this point, will the shipping costs even out over 4 different labels to match what the customer paid for the order, or am I going to be out more money on each label just to ship these to her?? Shopify needs to fix this issue and make it easier to navigate. If a larger order comes through, Shopify needs to know to offer create multiple shipping labels to fulfill this order. Shopify also needs Chat representatives to help us quickly with our questions so we can get back to taking care of our customers quickly.