When the base fare was < e-cert amount on pmUA, you simply had to call web support. They knew how to set the base fare to 0 and just charge you for any applicable taxes/fees. I don't know if the process has changed, but I'd suggest calling them first in the future.

I haven't had any problems using e-certs since the merger, and the e-certs now come with additional perks that didn't exist on pmUA. Also, e-certs issued by UA in the past do not come with a PIN number. Furthermore, you have to enter the e-cert number at the flight search page, NOT the payment page. That's probably the most common mistake people are making when trying to redeem e-certs, thinking they aren't working, and then getting frustrated by trying to book over the phone.