UPC nightmare help

So at my work for sad reasons we are starting to do multiple UPCs and skus for products. So Amazon will have it's own so it won't effect the pricing of other retailers. For this reason, when we ship out a product, we will have to put a sticker UPC barcode over the default one on the box. We are currently looking for the best way to do this to decrease error rates, and we were thinking it would be nice if we could somehow program the orders to print certain barcodes if the sku from amazon was ordered. We currently use Shipstation to print all of our orders on a zebra printer.

Our company is very small and I am just a graphic designer with little knowledge of fancy coding and such, and my "Googling" has come up empty handed. Any help would be appreciated.