You can't hold an itinerary with an e-certificate applied. What you can try doing (which as been met with limited success) is to hold the itinerary on the website, then call Web Support (not Reservations) and explain that you have an e-cert you need to apply. Ask them to keep the itinerary on hold - this is the part that may or may not work. If they do agree to keep it held, you can then complete the booking by phone or in person to use your paper voucher.

I tried this a few weeks ago and Web Support would not allow me to keep the itin on hold, because (as they rightly claimed) itineraries with e-certificates may not be held. Some agents may not read the rules and allow it.