there are normally two PNR's for this kind of flight. If you go to BAEC and try to do the seat reservation it will show the second (AY) PNR just before redirecting you to the AY site.
At this point go to AY site yourself and check the booking using that PNR. You should get the seat map.
This is how it works for me (BA ticket, BA flight number but AY operated) and it even recognizes my gold card and allows seat selection free of charge.