Oh, it'll take some time to master... I now have great respect for good photographers.
What you need to do is start playing around with the cameras settings and start braket shooting, this is taking a picture of a fixed item and then changing the settings and taking another picture etc..... Use the "A" setting and then dial your F stop all the way down, take a pic, then increase the F stop 1 setting, etc...
The larger the F stop settings the more depth of field you'll have
Don't even think about using the aufofocus, you have to use manual.....If I had know this I could have save myself several hundred dollars and not have gotten the AFS VR lens and just gotten a manual... Oh well
You have to use a tripod if doing macro, also use the self timer button to take the pics, less vibration and noise.
Here are the settings for the first pic
Lens: VR 105mm F/2.8 G
Focal Length: 105mm
Exposure Mode: Aperture Priority
Metering Mode: Center-Weighted
1/2.5 sec - F/20
Exposure Comp.: 0 EV