Two things: A "linked PNR" doesn't really mean anything. There isn't really any way to connect the reservations. It is my understanding that a "linked" PNR just means they put a note in your reservation that you are traveling with the other party - there is no actual combination though. Accordingly, someone on a "linked PNR" is really on a totally separate PNR and reservation and wouldn't get any benefits from someone flying on the original PNR.

Secondly, you state that you are using the credit card companion certificates. Technically, I don't think you are allowed to split the reservation although I have seen several posters in the CC Certificate thread mention that they were successfully able to do this by simply calling in to reservations.