I did this all online, for an upcoming QF-JQ trip; it took a few days for jetstar.com to bring up my itinerary with the JQ PNR, but it eventually took my details and allowed me to assign seats... so it can be done online (or at least it was in my case)... YMMV
I think the key for using it was to up the email as it was on the CMT site - QF online bookings for JQ coded flights have the customer email as
Nice, huh?