Everything described by the OP is normal when code-share flights are involved. The operating carrier will always create a so-called 'operational' PNR for its own flight booked as a code-share. The BA*AA flight is for information only in the first booking. AA created its own PNR for the flight that was booked as BA code-share, which is where the OP will be able to manage the flight online. It works the same way when booking flights operated BA under AA flight numbers - BA will create an 'operational' PNR for its flight booked as AA.
As to the two ticket numbers - are you sure that they are different numbers rather than continuation of the same ticket (where only the last 1 or 2 digits will differ?). That the 'operational' PNR contains only 2 flights is also normal - they need to see where you're coming from/going to next to monitor for any IRROPs.