I have had three surgeries due to CTS (right hand and both elbows).  The most important thing you can do is to listen to your body!  If your hand aches, stop for a bit and do some excercise.  Streach your fingers and arms.  Make sure you have a good chair and it it adjusted properly.  Does your desk have enough room for the mouse pad or are you reaching for your mouse?  Things like that will really stress your wrists and elbows.  Is your monitor at the correct hight and distance?  Looking up/down/sideway for long periods will stress your neck muscles, which will cause you to tense up and excellerate stress throughout your arms. 

About once a month, I sit in my chair, grab my mouse, close my eyes and just sit for a minute.  Then I check for any signs of stress in my body.  If my sholder is hurting, it usally means my chair is too low - adjustments are made and I do the same thing again till I feel "right". 

Once I bought a desk that had enough room to work on and a good chair, I have not had any more problems with my hands.  I take frequent breaks and do excercise throughout the day.  Remember, once the nerve is damaged, it takes years to heal - it's better to avoid the injury in the first place.

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