Printing & setup fees

Pad printing and set up fees would be part of the inventory costs, allocated to each item that it applied to.  So if the set up fee was $100, and you had 100 items, you would allocate $1 to each of the 100 items. 

Shipping would be part of the inventory costs if it is inbound shipping.  So if you paid $1,000 for 100 items and shipping was $100, then each item when you sold it would be $110 (depending on inventory method you used) When you sell the inventory, your shipping costs to the customer are separate and are considered shipping costs. 

Understood, so no need to try to separate costs on the invoice. Thank you!!

Correct.  Assuming all items are the same and have the same value.  If you have items of different values, then you would need to separate enough so that you can correctly value each item for when you sell it.