Here's my experience using MTM certs for the first time yesterday. Easy and fairly painless.

Background: I'm a Mosaic 3, status-matched late last year from DL Platinum, so I had 4 MTM certs. Wanted to use them for Mint on the new Dublin-JFK route, in late May. Only needed one-way, for two people, and was very annoyed by the possibility that 4 MTM certs would not be enough on a TATL route. But maybe phone agents could help me, which they did. So here's how it went.

1 - Checked on Google Flights for o/w prices DUB to JFK on May 24, 25, 26 (my possible travel dates) on B6, Blue fare. They were reasonable, lower than the other guys by far, in fact. But I still did not know if, once I'd bought a Blue fare online on one of those dates, I could upgrade both of us on only 4 certs. So I called the Mosaic line.
2 - Agent promptly understood the issue. What I needed to find out from her was, "Can you tell me the number of MTM certs needed on a given DUB-JFK nonstop flight, so I know before booking and can decide on which day, if any, I can upgrade both pax?" By making dummy bookings on my behalf, she was able to tell me that I would need 4x MTM certs/person on May 24, 3x on May 25, and only 2x on May 26.
3 - I asked her, on the same call, to book me + spouse on May 26, Blue fare, and immediately apply all my MTM certs for an instant confirmed upgrade. She did that seamlessly. I used a JetBlue credit card for 6x points, too
4 - We're both confirmed in Mint and good to go.

So, not bad. I was concerned the process might be a pain and not even work with just 4 MTM certs. Obvi YMMV but for me it was a breeze.