How do you handle being able to scan different UPC units of measure for one item record, for example, pens come in 25 each in a box and 4 box in a case each one has its own UPC

Multi-UPC support should do this. RF-SMART and other WMS solutions can support this

How can I enable multiple UPCs? The only thing i have found is WMS alias items

The clean way to do this is create UOM & BOM 1 pen - UPC1 1 box = 25 pens UPC2 1 case = 4 boxes UPC3 You can set defaults as one is a purchasing UOM, another as inventory UOM, and whatever is your selling by UOM. You will need to configure it correctly to convert to your standard Inventory UOM. I used to do this for a food manufacturer where they had single units and cases and pallets.

Where do you enter the different UPC ,what record type ?