Face Express is for the Departures side, I usually get scanned for the first part when I check in (Delta and JAL). You can then use the Face Express line to enter Security and then head to Immigration and then out. That also depends on if they're using it when you get there.
Arrivals works best if you fill out your forms on VisitJapanWeb and get the QR codes for Immigration and Customs. Depending on how busy it is the Immigration QR might save a couple of minutes. You should use the Customs one as soon as you get to baggage claim at one of their kiosks while you're waiting for you bags, then you should be able to use the e-gates on the way out. The Customs kiosk takes another picture for their system.