On Wayfair, SKUs works differently as on most of the other marketplaces. The SKU number is more of a group ID and can be the same for all product variants connected within one group.
The unique number added to products that can be used for quantity sync by the GeekSeller system is a Wayfair Supplier Part Number which has to be added to each product and cannot be a duplicate.
Please keep in mind that your GeekSeller SKU must equal your Wayfair Supplier Part Number for correct quantity and orders sync.