Once the buyer commits to buy the item and before he pays you will have the option to send an invoice.

But if the item is FREE Postage you cannot give discount on the item at all thru the ebay invoice. You can only discount up to the value of the postage fee if its not FREE postage.

Other than that the only other way you can send an invoice is via PayPal and for that you will need to know his PayPal email address. But to do that is seen as trading off eBay and is against policy. Because ebay would miss out on their FVF of course. Passing of email addresses via messaging is blocked by ebay.

If the price you have agreed with your buyer is something other than the listing I think the only way you can do this is to have him buy it at the listed price and then do a partial refund thru PayPal for the difference. He will have to trust you to do this tho.

But keep in mind you will still pay FVF on the price it is listed for not for the discounted price.