Under the default settings it would seem Sonar automatically chooses zero crossings when you drop the clips together into one track. Might be you method of trying to use mutiple tracks would cause the clicking so try using one track instead.
My method is to insert an audio track, clone it a few times then start recording.
I use the split function to divide into the good clips. I delete all unwanted clips to keep it tidy.
Set "SNAP" to whole or half measures first to retain timing.
Now assemble this into one track. I never get any artifacts unless a note sustained past a split.