Log into your Paypal account and find the payment, click on it to call up the payment transaction page, bottom right of this you'll see a button that says "Refund this payment".
Click on that, and change the amount showing (which is the full amount by default so do this carefully) to the amount you wish to partially refund.
Double check that it's correct, then authorise it.
Be aware that eBay don't issue partial fee credits.
