We recommend you allow our system relay on your numbers from Shopify, and cancel incoming orders if you do not have enough qty on Shopify. However, we understand that you may not have an updated qty on Shopify all the time. This is why we added an option which allows you to turn off / on auto cancelation of orders based on Shopify qty.
Cancelation should not happen often, since we keep your qty in sync between Shopify and GeekSeller, but it may happen for different reasons (for example JET/Walmart API is slow or down and cannot read our latest qty update).
The option to turn on/off auto-cancelation can be found in the settings of your GeekSeller panel.