I have booked with BA and they use AL for the shannon-heathrow bit. I cant book in online for the shannon bit but can for the heathrow - vancouver bit, ie print boarding passes etc. However I am a bit worried this might muck up the check in at shannon as I want bags checked in all the way to vancouver. By getting passes online I can save hassle. BA wont answer the phone!!
I flew Dublin - Heathrow - NY last year with BA (Aer Lingus for the Dub-Heathrow leg). I checked in online on the Aer Lingus site for the Dub-LHR leg, and there was no problem checking the bags through.
I returned Miami - Heathrow - Dublin (again AL for the LHR-Dub leg) and did the same - checked in online on the AL site for their bit, and on the BA site for their bit. Baggage checked through without a hitch.