yes, the zero crossing is critical. Aviods the "pops"
As I become more familiar with Sonar (7 months so far) I have begun to realize that even when you are not using any midi, setting the appropriate tempo and time signatures (and key) is key. Then if you want to loop, stretch/shrink, or in anyother way adjust the clip to fit with your intentions it will be much easier. The downbeats will line up, so it will be easier to place clips and when you expand or shrink tracks it will be in time.
The biggest drawback of this is when playing to the click track I have the tendency to play a bit stiff. You need to find a balance. I try to "block out" the clicks during certain parts in my head and at certain points check to make sure I came back on the beat. Sure you can map out the increases and decreases beforehand, but sometimes they happen naturally. Then I need to go back and try to adjust the tempo settings later.