I've seen reservations made by my corporate travel agency which have three separate PNRs associated with them, unfortunately. One which is their "own" and which calls up the itin in the "Virtually There" site; another which belongs to the operating carrier (i.e. UA), and a third for the codeshare partner whose flights were booked (i.e. US, when the travel agency booked me on US flights operated by UA, for example).

It can be a pain to keep them straight.


Edited to add:

Also, if you need the e-receipt for various purposes (tax, employer reimbursement, etc.), you should get a copy of it ASAP--I usually also get one at the airport if I have time, from Mr. Easy Chicken.

Why? The e-receipt for past flights I have found can change / deviate significantly, if it works at all. I've had it claim a flight I took was $650 when it was actually $250, for example. Obviously, I wouldn't use the $650 "receipt" for any reimbursement purposes, but wow, imagine if you needed the receipt and couldn't get the right info on it!