setting song start and end points?

Welcome to the forum.
Does the SONAR project have long periods of silence at the beginning and end?
When you play the song in SONAR, does it stop at the end of the clip or continue past it?
In any case, you can import the .wav file back into another SONAR project, use the Split tool to snip off excess clipage, delete those empty clips, drag the entire remaing clip to the beginning of the track, then re-export it.
Or, after importing, select the track then drag the cursor across the Timeline where there is no sound, thus selecting them for editing, then pressing the Delete key on the computer keyboard. Drag and export as described above.
Uh, I guess I should have asked which version of LE you have. If X1 LE, the steps may be different.

Be sure to set the project options to stop at the end of the song automatically.  That usually solves the problem.  the software then looks for the last bit of audio or midi in all the tracks and stops automatically when it finishes playing it.  It does NOT stop automatically if you are in record mode for obvious reasons. 

Next, I always leave 2 complete measures at the beginning of a song for count in while it's rolling. 

Remove any audio or midi notes that are past the end of the song. I often will drag a clip past the end of the song while I paste something else in the hole to try. If it works I delete the clip I was saving. 

In reality, I don't worry about the silence at the beginning or end of the song.  I export the song as a wave and then I open it in my Wavepad Wave Editor and trim the silence off the song and save the edited song. 

I leave 500ms of silence before the song and enough silence at the end for the reverb tails to die out completely. The editor doesn't care if I'm trimming 1 second or one minute.