You don't.
If flying to an APIS destination, and you are issued a boarding pass, you will not have to check-in again because you are already checked-in.
The boarding pass will get you all the way to the gate where the spot check of your passport will occur as usual.
In rare cases, you might be issued a gate pass to get you through screening but unless you're OK to board, no one wants you actually in the terminal.
I imagine it's possible for some uncommon nexus where it's easier to issue a BP and check at the gate.
