You post is confusing to me because first you say "
2 identical tracks", this implies this is the same piece of music that you copy and pasted or imported from outside of Sonar.?? true??
But then you go on to say "There are parts you want to record to the other track"?? This now implies the tracks are not the same. And "recording" to an already recorded track is not the way you work in DAW land, you copy and paste pieces you want into a new blank track or paste into an existing track overwriting the unwanted parts. There are many options for editing multiple tracks into one "best of" track.
If they truly are identical, then just import it once and then
clone that track. You can do this over and over and it will be perfectly lined up.
If what you have is say, 2 guitar tracks you recorded that are not lined up then you have soundcard driver timing issues.