The way it works for me is: Shipping cost is from eBay. (Listed under shipping service used) You can not change this value.
Actual Shipping has a entry box, (a few lines down) where you enter the postage that you actually paid for.
Buyer pays the shipping from the listing, say $3.41, and when you buy the postage using the print label functions on eBay, they give you a discount. So maybe only $3.01 is actually withdrawn from your Paypal account for this items postage. You save $0.40. I enter $3.01 in the entry box provided.
However: the reporting system in GS does not figure this entry box value correctly.
Hope this clears it up.