your ruler should be perpendicular to the focal plane not 180 degrees across it.
you want to use the marking in front or in back of the focal point to note front of back focus.
you need a tripod with the camera at a 45 deg angle to the ruler/focus chart
ideally you want more contrast than that ruler provides as well and you need very good lighting, (I go outside midday)
a quick google search came across this:
http://www.tunerphotography.com/uploads/Instructions_for_using_the_AF_Fine_T...ocus_Chart.pdf
there are several other websites that give you instructions as well,,, pay close attention to the image on page 2, that's what a focus check image should look like
also remember that when you focus on an point, roughly 1/3 distance in FRONT and 2/3 distance BEHIND that point will be in focus. that will be the case no matter how shallow DOF you have