I was in the same situation a few years ago, so this is from memory. Filled up usual custom declaration (on a machine). Waited for my luggage, went to claims desk and filled up the airline form. On this form you need to indicate if you have any dutable goods. I indicated so, the airline told me that they will not deliver my luggage home - I will get a phone call when it is delivered, and would have to come back to airport and clear it through Customs myself.
When passing the Customs, I presented the declaration and the claim paper from the airline, and was referred to the second screening. The Customs officer at the second screening asked a few questions about the nature of the goods, made some notes, and said I'd have to come back. It was delivered next day and I got a call from the airline. Came back to the airport (there's a CBP office on Arrivals, you do not get to the actual baggage carousel area). I think I filled up another declaration and signed some other form, signed the airline form confirming I got my bag, and got my bag.
Again, this is from a few years ago and related to SFO airport. No idea how this would work if you have a domestic connecting flight.