Hi RAGIII.
You're experiencing a problem that photographers who dabble in Macro Photography battle with constantly. And also those of us that photograph birds and other animals.
In Macro, we want sharp focus front to back, but due to physics that's not possible. And the higher your magnification and the closer your subject, the more extreme the problem.
With long lenses and wildlife, we battle with lens shake and the camera focusing in front of or behind the eyes of the subject.
There are two things that can help you with your specific problem.
1. Lighting. The more light you can put on your subject and the more diffused, the better your camera will be able to focus. I always use manual focus for my macro, but if you are using A/F, try to set your camera to a single focus point and use the toggles on the back of the body to move the focus point to where you want it.
2. Use a tripod. Always try to keep your camera as still as possible. That way, if you need to close the aperture down to F/16 or smaller, thus slowing your shutter speed, you can maintain a steady camera and avoid softness due to camera shake.
3. Focus stacking. If you have Photoshop, then you can take more than one image on a track focusing at different points and then blend them in photoshop to get a broader depth of field.
Best of luck,
Hugh