You check in and out of Cruz Bay, on the west end.
Cruz is jam-packed and not the best place to anchor. Too busy.
It's easiest to pick up a ball in western Caneel Bay near the point, throw everyone in the dingy and tie up at the dingy dock, which is at the head of the ferry dock in the center of Cruz. Everyone must go, and take your passports directly to the custom's house, which is north (to the left) of the dingy dock.
The dingy ride can be a little splashy sometimes. Depends on wind.
I posted a sticky with links to C&I forms and maps a few years ago at this
US C&I TTOL LINK