Yes, we want to track both the shipping income AND the shipping expense. I prefer to isolate my shipping income, by creating a correlating income account called "delivery income" or "shipping income" ..then down under my COGS section, I will see my shipping costs. That way you will be able to see if you are making a profit on shipping, or if you are losing money on shipping.  

If you set up your customer invoice item to go only to an expense acct or COGS account, then what you are really doing is REDUCING your expenses or COGS totals on your Profit and Loss report. You actually can set up one item to cover both shipping purchases/expenses and shipping income by clicking the box that says "this item is used in assemblies or is a reimbursable charge". It sounds like you pay someone else to ship your products, and then funnel that cost onto the customer invoice to be reimbursed, so that is considered a "reimbursable charge". 

Once you click that box, you will see 2 options now, on the left, it will have you assigning a COGS account  to PURCHASE TRANSACTIONS, and then you assign an acct for SALES TRANSACTIONS, this is where you put in your Income Acct. 

Hope that helps! I tried to add screenshots to this but it wouldn't let me. Best of luck!