Another very simple approach might be to take a series of shots with increasing f stops. As your numerical f stop goes up, the size of the aperture opening goes down. Wide open, you will get a very narrow depth of field; while smaller openings yield greater depths of field. This is very basic, and should have been explained in the reading that has already been suggested.
Try it for yourself and see what happens. At least part of your solution may be as easy as using the appropriate aperture for your subject. This, plus other tips already discussed, should help you greatly.
