Shopify POS Pro-Shipping from POS locations and placing Ecomm orders

Hi all, hoping for some guidance. We have a main inventory holder, and Shopify Pro for our ecomm and five pos locations. We have transactions where we place orders online, or ship purchases from our retail locations. Currently, if have to ship something from a store, it automatically marks it as shipping from our main warehouse. We have to place online orders for customers on the actual website, like anyone else would. This is clunky, time consuming, and messing up our inventory. Does anyone have a process, or configuration, that work for you in a similar situation? We don’t have fulfill from multiple locations turned on at this time-we can, but I need more than being able to fulfill orders for ecomm. Thank you in advance!