Does the USPS have a preference? There's no official answer to that, but here's what we do know.
Because PO Boxes are at the post office, delivering mail there is as simple as taking it out of the bag, reaching over, and putting it in the slot. That may be a bit of an oversimplification, but it drives the point home. With PO Boxes, the USPS doesn't have to transport the letter to a separate location. Therefore the delivery that costs the least in terms of labor and time is the Post Office Box delivery.
So, if you have a preference, use only the address that you want it delivered to. Don't use both addresses unless you really don't care where it goes.
Caveat: Some rural locations and small cities only have PO Box service, i.e., the residents don't receive mail at their physical address. In these cases you'll have to send to the PO Box. Sorry. To find out if an address is USPS deliverable you can use our address validation service before dropping it into the mail.