As shown in this page,
http://www.ana.co.jp/wws/japan/e/loc...n/checkin.html
At Fukuoka, You can make thru checkin at checkin counter No.8.
When checking-in at the airport
International connecting counter number at airports
Sapporo 18
(Chitose)
Nagoya K1
(Chubu)
Osaka 11
(Itami)
Fukuoka 8
Okinawa 8
(Naha)
And, in my experience, even with separate tickets, ANA can make thru checkin. However, untrained agent may not know how to handle separate tickets. In such case, you have to ask help of supervisor.