I think the thing to do is book it on a single PNR and then call back and have it split. As far as I can tell, the computer doesn't know that it was booked with a companion cert once it's booked. You don't even need to mail the thing in, even though they say to. I never have, and it hasn't been a problem.

I wouldn't think that upgrades would be a problem, and you definitely accrue EQMs, even on the companion tickets.

I doubt you can book an F and get 2 Y.

Perhaps someone has more direct experience with what you're trying to do, but I hope that helps some.

Eric