As said, shoot in RAW if you can at all, that'll give you the best flexibility for editing afterward. Don't bother with setting to B&W on the camera or anything like that, just remember it's a one-off event, never to be repeated, you need to capture it then and there.
For group shots, or anything with more than 1 person in it (especially if it's a child) take lots of shots, even if they end up very similar, because hopefully one of them will have caught the best expression or pose. It will also give you a chance to produce a compiled shot in photoshop later if you can't get one perfect photo. See below.
Kids move a lot and you need as fast a shutter speed as you can manage in the church.
Traditional church buildings are generally quite dark, (unless you have a lot of sunlight coming through the windows), so manually set the ISO higher (up to 800+) which will enable you to have a higher shutter speed (you want at least 1/30 to stop people being blurry even if they aren't moving). Note that upping the ISO will give you more noise on the image but if you use RAW you can probably get around that in the editing.
Ignore your flash, on board flash will produce nasty light anyway, you wouldn't be happy handing over photos with that.
Also try to get physically close to the action (thus avoiding zooming too much) this will mean you can have a wider aperture (lower f-stop) and therefore a higher shutter speed.
Here's one I took last Christmas, I actually took about 6 shots, and this was a photoshop of the two best ones.
Taken with a Nikon D60 with a flash bounced off the ceiling.
