File Naming on the Nikon D3000
As far as I know you can't. If you shoot one of them in the sRGB color space they will start with DSC. If you shoot the other one in the Adobe RGB color space that will start with DSC. What I suggest is that you save them in different directories or rename them when you upload them to your computer. I use Nikon Transfer to rename my pictures to sensible names when I copy them to the computer.
You can also change the comment on each camera to embed the information in the EXIF information.
Does anybody know if you are able to change the beginning prefix, such as "DSC" 001, on the Nikon D3000? I'm looking into purchasing two nikon d3000's for event photography but i need to set one camera with a different beginning prefix than the other so i can tell which photos are to which camera.
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