It is not clear what you are trying to do? Are you trying to encode each component separately?
That can be done, depending upon your software. JPEG is oblivious to what is being compressed. It can't tell a Y, from a CB, from a B. The question is whether your software will allow it.
Each color is encoded as a separate scan. If you parse a compressed JPEG file, it is is simple to separate the scans for each color component.
The way you could probably do it is try to fake the encoder into compressing each component separately as a grayscale image.
If you are trying to do 1/3 of an image at a time, you'd have to break the image up yourself.
You might also want to look at progressive JPEG.