Handling photos for syncing can be tricky. Make sure you import the pics from you iPad to your computer first (into iPhoto, or something similar). Arrange them into files and name them as you wish. Then, select those files as well as any additional when you sync, they'll be put back. Otherwise they will be removed and lost.
Other members may have better tips, I haven't played with photos much, since I lost a bunch on my first attempt. I didn't have them backed up this way yet.