Tried to search for a while but couldn't find an exact answer.

I'm planning a graduation present trip for my girlfriend. I have an award flight for her on LAN leaving from JFK. I will be purchasing the leg from SFO-JFK as it wasn't available. I would like to add this purchased flight to the award PNR so that when she checks in with AA in SFO it will be seamless for her and AA can just check her in for the whole trip. Is this possible to do? Can I purchase the ticket online and then call to have this done or should I purchase the ticket through an agent on the phone who could add it to the PNR?

If my research on this forum is correct, it seems that it is possible to have AA check her in for the flight on LAN when she checks in for the AA flight in SFO (right?), but I would rather not do this as it will be an added layer of confusion for her in explaining how to do this and why she has to do it.

thanks in advance!