How to take good photo for cristening?

I'm taking a feww good photos to a friends child christening. The photo would not have any extra lighting just natural light through windonws which is not enough. How can i use autofocus on my nikon d3100 in ordern to capture good photos since he baby its gonna be moving? And which mode to use my nikon sb 600 speedlight? How can i use autofocus and speedlight together. If i put the speedlight in auto mode it will do all the work?

I don't understand your connection between auto focus and using a flash. Sometimes auto focus has problems locking on in very dim light, but I doubt the lighting will be that dim. Also you said there would be no extra lighting. Last I heard, a flash is not ambient light.

If you are unsure what to do, put the camera on program and the speedlight on TTL and fire away. Consult the histogram to avoid blowing important highlights and use exposure compensation to adjust if necessary. If you can bounce or diffuse the flash (or use it off camera, but I'm not sure if the D3100 has commander mode) you will get much better results. If you have a fast lens, like the 50mm f/1.8, use it rather than the kit lens. Wider aperture is better in low light, but beware the shallow DoF.