What is the best way to receive a refund from a seller when they are out of stock but have offered a refund?

[freightcar2009]

I recently bought a few parts for my car from a seller however they have informed me they are out of stock for the side skirts.  At this stage the seller has done a good job with the service and offered a refund.

I am just wondering the best way to organise this, my instincts tell me I should put in an item not received with Pay Pall and organise it this way rather then letting them just do a direct deposit, this way they wouldn't be charged commission on the product.  Is this the best way to do it or is there a better way?