When you head back from Nusa Penida to Bali mainland, all you need to do is be at the Harbor 1 hour before departure time. You need to register your departure details to the closest Fast boat office, available close to the Harbor. Ensure you have got your return boat ticket otherwise, you need to purchase it advisably 2 days or by the latest 1 day before the departure date to avoid being fully booked.
From Nusa Penida port the fast boat hits the sea to Padangbai / Sanur Harbor in 30 minutes ride.
If your boat tickets are booked with complimentary shuttle service to your following accommodation, ensure to get on the official transport/vehicle service from the fast boat company. Otherwise, there are many freelance drivers in the Harbor who will try to offer you their service with some negotiated charges.
Here's everything you need to know about how to get to the Gili islands from Bali on a budget-friendly way boatbalitogili.com.