I don't think there's any technique involved except having decent eyesight. With time the eye gets "educated" to see the needed details to distinguish what is or not focused, but still even in the beginning anyone with a good eyesight should have a better keepers rate than that.
The mirror you see when you take the lens of your camera is the mirror that reflects the image to the viewfinder and that's the mirror that can be misaligned.
So, behind that mirror there's a eccentric bolt (two actually, but the other is for the AF sensors, forget the other, you only need the first for this), that bolt aligns the mirror so the image it reflects is aligned at the same plane of the sensor.
The easiest way to check it is to get the fastest lens you have, preferably one that focus very close, a macro lens is about perfect. Put your camera on a solid tripod, get a ruler, focus manually on any number, keep the lens wide open, put the line referring to the number at the exact centre of DOF on the viewfinder, if the mirror is misaligned the resulting image will have that dof decentered from the line you focused on. If that's the case you'll need to either send the camera to nikon, or mess with that bolt until it's right. I'm a DIY guy so you know my choice
Here's a link that explains all this better:
http://www.leongoodman.com/d70focus.html
The article refers more to the AF part, but the process is nearly the same.