Hi Imposter
Nobody else has answered so I'll give it a shot. Generally n-Track's midi function is not regarded as its best point.
I'm not entirely clear about your question, but:
Have you set the midi tempo to match that of the recorded parts? And line the audio parts so they synch with the grid. (This may be impossible!!) Also there is a whole range of grid settings on the drop down grid menu that might help. Also you can turn the quantize off so that your notes stay where you put them and don't snap to the nearest grid line.
It's a very fiddly and frustrating job though - most people find it easier to do the midi parts first then track the audio whilst replaying them. As it is, the easiest way wil probably be to play back the midi part once you've programmed it, record it, then juggle the resulting audio file to fit in with the timing of your other parts.
Hope this helps a little bit - apologies if it doesn't.