Online check-in is available even if you have baggage to check in.

After completing online check-in in advance, please drop off your baggage at the airport baggage counter or the Self-Service Baggage Drop machines (available only at Haneda, Naha, and Fukuoka Airports) on the day of your flight.
Please drop off your baggage early to ensure you can pass through the security checkpoint at least 20 minutes prior to departure.