I'm talking about the 3 boxes that form a column, near where it says 5V on the top of a lead and 3V below it. The lead comes out of the middle box.
The datasheet for the AT90USB1286 mentions nothing about this, only that there should be 22Ohm resists between D- and D+ (check) and a 1uF cap to UCAP (check).
USB1 supplies 5V (default usb power).