final cut pro, with shake and motion.
 

I edit using final cut pro. When I want to put a clip into motion or shake should I right click the clip in the timeline and use the sent to option or should I drag the original quicktime movie file into shake or does it matter?

Short answer: Send to works just fine

Long Answer: Depends on what you are trying to do... Some tasks are better suited to being done as a stand alone operation rather than as part of that particular workflow. Do some tasks to start out with both ways to learn what works better each way and use that info to gauge your workflow in the future.