Partially Fulfill a PICKUP order

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We have recently added the new feature "In Store Pickup" that Shopify has introduced, but we are unable to close Partially Picked Up Items on Orders. It is becoming a headache having to track each orders status and maintain proper inventory. In the past we were using the shipping methods and labelled one as IN STORE PICKUP, but given the logic used this item shows up at the top of the shipping options as FREE Shipping and we were receiving too many calls from customers who misread the option and assumed it was Free Shipping to their door. With the old method we could easily fulfill line items completely or partially as they were provided to the customer. Our business produces custom products for people and not all of the items are available at the same time, but our customers may prefer to pick up some parts vs. waiting for the full order. Can someone please help me with fulfilling these new pickup orders partially.