An off-center split prism should work fine to assist manual focusing at the spot it's located. Lens resolution tends to drop off toward the edges. So the farther off-center the focus point, the lower the resolution at which you'll be able to focus. You can still fallback on autofocus if your lens supports it because the autofocus sensor is behind the mirror and not affected by the focusing screen.
Whether a modified focusing screen will affect other functions depends on the location of the sensors with respect to the focusing screen. On a Canon EOS 550D, for instance, the autofocus sensor is behind the mirror, and the light-meter sensor is behind the focusing screen, so using a focusing screen that transmits less light than the original will result in over exposure, while a focusing screen that transmits more light will result in underexposure.
A split prism over the center spot meter may affect readings by reducing light transmission or changing the path that light would normally take if the prism weren't there. It may not be significant if the difference is only a fraction of a stop.