I have a sample that is in the key of A and was recorded at 88 BPM.  At 88 BPM it plays over 4 measures in 4/4 time.  I want to use Sonar to take that sample and change it to the key of C, have it at 100 BPM and still have it fit in the 4 measures.  I can use stretch it using the clip editor to change the pitch to C.  How do I take this sample now in the key of C and make it so that it is a 100 BPM sample that still fits in 4 measures in 4/4 time?  If I go into Clip Editor and change the new C sample from 88 to 100 and save it as a sample called C100 and then bring it back in to a song that has 100 BPM the clip is no longer with in the 4 measures (it goes pass this).  What do I need to do to make this work?

Easiest way is to convert it to a loop then adjust the project tempo and key.
 
Put the clip in an audio track. Select the clip and do ctrl-L. That changes it to a loop, or "groove clip" in Sonar-speak. Double click the clip to open the loop editor. Find the entry for number of beats and enter 16 (for exactly 4 measures). Enter 'A' for the root note.
 
Then go to the beginning of the project and set the project tempo to 100. Set the project key to 'C'. Move the clip around to align it to the measure/beat you want.
 
If you save the clip, it will now work at any project tempo and key.