If you want more DoF, you can stop the lens way down and add light with a flash, use
a tilt-shift lens on extension tubes, or use software and multiple images focused at different points to
focus stack.
Focusing with a macro lens is hard. Most of the time, focus is set by varying your distance to the subject. You can also try using the autofocus confirm, if you think the AF is going to be more accurate than your eyes through the viewscreen. Basically, half-press the shutter button, and turn the focus ring on the lens, and when you hit the point the AF system would use, one of your AF points will light up. (I think it's green on the Nikons. It's red on my XT).