I just tried to apply a $75 e-Certificate from the 5000 miles promo to a DEN-LAS RT for $98.30, theoretically leading to a great fare of $23.30 RT all-in. Surprisingly, it priced out w/ certificate to $83.30. I called CS who was surprised as well and after 4 transfers I learned:

While it is possible to overpay with a paper certificate (and get a certificate with the difference back), you can't do that with an e-Certificate. It has to be used in full or not at all. So, when the base fare is less ($72.55) than the e-Certificate, you can not use it. The frustrating thing is that I didn't see that restrictions in the T&C of the promo. Any ideas of how to use it anyway?