Using aliases to count orders for one SKU as orders for another SKU? That will help with your reporting and your product settings, but you'll need to make a couple changes in the HTML packing slip editor if you don't want the original SKU to show up on your packing slip.
*Please note that you must be on a Silver or above plan to customize packing slips using the HTML packing slip editor.
Head to your Account Settings (the wrench icon in the upper right).
Next, select Templates and then Packing Slips from the sidebar on the left.
Find the row for the packing slip you want to customize and click Edit. (If you use the default template, you will need to Copy it and customize the copy.) When the HTML editor appears, click on the Order Items section and look for the [Product Sku] field replacement.
Remove the field [Sku] and replace it with [Product Sku] to use the alias-linked SKU instead of the original SKU.
Your screen should look like this:
Don't forget to Save your changes! Packing slips using this edited template will use the alias-linked information rather than the original information.