Chris,
First off, I am not a "camera pro" (far from it!

) -- but that is another hobby I've "dabbled with"...
I believe you need to increase your "depth of field". The best way to do this is to increase the "f-stop" setting -- the larger the number, the greater the depth of field. (f2 = wide-open lens = narrow depth of field... f32 = really "shut down" lens = much greater depth of field.) The reciprocal of this is that you need to increase the amount of light on the subject, decrease the shutter speed, or a combination of both. With a decrease in shutter speed, the use of a tripod and a remote shutter release cable becomes necessary.
This is one area where my old, trusty 35mm camera had it all over my "newfangled" digital camera -- other than increasing the amount of available light, I have no idea how to accomplish what I've noted here... And I have a sneaking suspicion that it may well fall to the realm of the "high-end" digital SLR cameras, with interchangable lenses and many of the features of the "standard" SLR camera.
One idea comes to mind... I don't know if you happen to also be a collector / modeler of 1:1250 scale / 1:1200 scale ships... There is a fine gentleman who is a "mail-order" retailer of these ships, whose name is Chris Daley. He has a website:
http://www.1250ships.com/index.htm
In the left-hand "navigation panel" is a link called "Features" -- click on it for one of the best descriptions of "miniature photography" I have ever seen. Chris' photographs are REALLY good! I have corresponded with Chris many times, and he has been very helpful to me with hints / tips on photography... I also have purchased several models from him (as this "genre" is another of my hobbies!).
Hope this helps!
Regards,
Tom Stockton
"Well, I've been to one World's Fair, a picnic, and a rodeo, and that's the stupidest thing I ever heard come over a set of earphones. You sure you got today's codes?"
-- Major T. J. "King" Kong in "Dr. Strangelove"