Apps to Bypass Double Shipping on Orders Split Between Two Locations?

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We currently have two locations in the city with different items, but they are all shipped from the same location. We are currently putting majority of inventory in the location from which we ship from.

We want to integrate our POS and Shopify. However, due to the double shipping for anything under $99, it is not feasible. Are there any apps that can help us bypass this issue?