No offense intended, Nat, but without the detail you provided in your subsequent responses, your original post wouldn't have been very helpful to anyone. And it wasn't unreasonable to conclude based on that meager initial contribution that you had misunderstood the goal.
The fact remains that, by itself, Melodyne cannot align a SONAR project's timeline to audio - extra steps are required. And if the project contains clips that don't start at time zero (as in this case where the song starts on a pick-up note), you're going to encounter more issues when you bring in tempos from a MIDI file, which, incidentally has to be done by copy-paste after opening the MIDI file as a new project; it's not actually possible to 'import' a tempo map directly from a MIDI file to an existing project.
The Devil on the Highway to Hell is in the details.