Hi Leegold!
You have to set the aperture fixed in your camera to "1.0" and use Av mode. Then, the camera sets the right speed for the aperture you set manually in the lens. Since the manual lens were designed for 35mm film, smaller sensors like the Foveon X3, trend to overexpose when the lens is wide open due to the parasitic light going around the sensor. Some people is doing some kind of "jackets" on their lenses to reduce the diameter of the back lens.
Regarding the Autofocus, I understand you mean the focus confirmation, because there is no way to autofocus with manual focusing lenses...
Not sure how it does work. On other cameras, like the Canon or the Olympus, there are "chipped" adapters that mimic the behaviour of the AF lenses for this. I haven't seen any chipped adapter for the Sigmas, this might be for one of two reasons: Either it's supported by the camera with no chips (like in the Pentax) or there is no way.
I'll be trying it on my SD10 to see what happens with the M42 ones (I cannot recall it at this time).
Regards.
Jes.