How can I manage different stock and SKU codes for POS and online stores?

Shopify Partner
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We have different stock and SKU codes for our POS Store and our online store, they are technically separate but are under the same brand name. I am finding separating the stock very complicated as we sell similar products so they are easily confused on the backend of Shopify. Also for the online website we have categorisation processes that arent needed for the POS store. 


We have shopify plus, so would it be easier just to create a separate store for the POS and keep my original store for my website? How easy is it to transfer the data to a new store? 

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