Hi nightfox
We don't have any integration with Square. But if what you need is to separate your stocks for all your products in different inventories (online and offline), you can do so with Multi-Inventory. Just that when you sell any item offline, you'd have to create the order manually in WC or deduct the stock for the product yourself. Or, alternatively, you could find a developer that can help you to integrate both (ATUM and your Square system).
Best Regards,
Salva.