This thread hasn't seen any action in a while, but I just had fantastic success getting a "one time exception" in booking 3 PAX with 3 e-certs on a single PNR via web support. The call went something like:
Agent: Thank you for calling united, how may I help you?
Me: I'm trying to book a flight on the website for three passengers with 3 e-certs, but the website will only let me enter a single e-cert.
Agent: I'm sorry sir, you can only use one e-cert at a time. You will need to make a separate reservation for each passenger.
Me: Oh, I see. The problem is that one of the passengers is my 2yo daughter and the website will not let me book a flight for just her. Would it be possible for you to make a single reservation with me and my daughter on it, and then I'll go to the website to book my wife's ticket on a separate reservation?
Agent: I understand your issue. I will go ahead and make a one time exception and make the reservation for all three of you.
Me: Woohoo! (ok, more like "thank you", haha)
It took him about 10 minutes and a few holds, but we are all booked.
When it came time to give my CC#, I thought I would push my luck and ask about making a partial payment with a gift certificate (an actual gift card, not an e-cert). The GC says "Cannot be used in conjunction with an Electronic Travel Certificate", but I figured it can't hurt to ask. The agent seemed confused and said "but sir, I've already applied three e-certificates to this reservation and you only have three passengers". I explained that it was a GC not an e-cert. He put me on hold to call his support desk. He came back about 2 minutes later and informed me that the GC can only be used on the website, that his system had no place to enter it... Oh well, I still consider this to be the smoothest and most successful UA web support call I've ever had. ^