If a manufacturer assigns an existing product a new UPC or if you want to assign a Product Lookup (PLU) code to an item you can do it by adding in a new reference code.  Reference codes must be unique in the system and must be numeric.  Typing a reference code into the Point of Sale search will return the single item mapped to the code.

Steps to add a reference code:

Look up the item, by pasting the current UPC in the search box.

Double-click on the result to bring up the item edit screen.

Once on the item edit screen click the Reference Codes Edit button:

Enter in the new UPC or Product Lookup Code (PLU) and click Add New. 

If it's a valid UPC and it's the UPC that should go on outbound orders, click Set Primary UPC.

Press OK and then Save on the overall edit screen.

Merging Items -

If the UPC you enter is already attached to another product, it will ask you if you want to merge that item into this one. By merging, it will pull inventory and sales history of the other item into this item and mark the other item as unsearchable.
This is potentially dangerous, and irreversible, so please use care when merging items!

See here for a more specific detailed tutorial: