Neither you nor the seller can mark this as paid - you have to pay through Ebay, not bank transfer (unless it was a motor vehicle).
If it was not a car and you paid for another item without using Ebay checkout, you won't be able to use the Money Back Guarantee should you need to. Cars are not covered by the MBG anyway.
"There are two ways to be fooled. One is to believe what isn't true; the other is to refuse to believe what is true.”
Søren Kierkegaard, Danish philosopher (1813 - 1855)