Alex Anderson once had a Doctor on her show that use to air on HGTV. She showed examples of how to quilt properly to avoid Carpal Tunnel and back problems while sewing on a machine and also hand quilting. Here is a list of things I remember that she said.
1. When sitting in a chair, adjust the chair so you knees are the same height as your hip bones.
2. Try to keep your hands level with you elbows (or the same height) when sewing on a machine or hand quilting.
3. Make sure you keep your wrist straight when hand quilting. The Doctor said this was very important to keep from getting Carpal Tunnel. She mentioned that a lot of quilters bend their wrist when quilting. This is really bad for your wrist and fingers. So check to see if you are doing that and try to change that habit if you are.
Your thumb, pointer and middle fingers are the strongest so try to use only them. I started quilting with my thumb since its the strongest. It's a little different since you basically quilt away from you instead of towards.
Doing these things have really helped me. I also applied these habits to when I am sitting at the computer.
I have a small exercise ball that I bought from Walmart. It helps to strengthen the muscles in your hand to help them from being damaged. But since you already have Carpal Tunnel you might want to ask the Doctor about doing that first. I hope it gets better.