When I first started my career in CAD, I had so many issues. Mainly sore back and aching wrists.
I ended up going to the physio and it turned out that I have a wonky pelvis. I now sit with one cheek on a folded towel and the other just normal and all my back pain is gone.
My wrists is much more difficult to fix, although it is a lot better than they were.
In most cases your issues will be posture/how you sit. I can tell instantly if a desk is not the height I am used to by millimetres, because the pain starts to come back.
You should always use a desk that supports your full forearm for your mouse, corner desks are good for this.
I switched to a huge mouse (google handshoe mouse) and an A3 paper sized mouse mat. Then whacked my mouse sensitivity down to force me to use my arm to use the mouse and not my wrist.
Here's my number one tip though, and you might think this is crazy.
Switch your middle and right mouse click with some third party software.
This almost instantly relived my hand. The reason why is this:
Particularly in AutoCAD you spend a lot of time panning. To pan we hold down the middle mouse button and drag. The spring on this button is usually stronger than the normal buttons, so you are pushing down with more force and holding it there whilst panning. By switching the buttons you now use much less force AND you insure that your coworker can no longer use your computer! I've been doing this for about 13 years now and it only becomes confusing when you have to tell someone else which button they need to click to solve a problem!
I use X-button mouse control to switch them, other software may also be available.
9 times out of 10 though, it's your posture and your setup causing the pain, and if you live in America, don't let your Doctor tell you that it's carpal tunnel. You'll have the surgery and 3 months later the pain will be back. It's almost always RSI.

Expert Elite

Inventor Certified Professional