If seller is sending as one item, then it is up to him to refund any overpaid postage. There is no system for getting this refunded, it is between buyer and seller.
It is even possible that seller has no idea what to do, but you should ask, and as a last resort you are able to leave feedback, but do not use this as a threat, as it is not allowed and could be removed on request to ebay by seller.
