Removal of the nut that you show, which is jammed on the threads, could be done by clamping the unthreaded body of the stud in a vise and using an impact wrench on the nut. If you don't have an impact you can clamp the stud in a vise, put a box end wrench on the nut, and impact the wrench counterclockwise with a hammer. Or you can put the frozen nut in the vise, put a vise grip so tight you can barely close it on the unthreaded stud CLOSE to the threads and hammer the vise grip counterclockwise. I would not mess with the block end of the stud and, if you do, you may find that the length of the stud, by torsion, absorbs the force you are trying to apply to the stuck nut.
You could also, for about $30.00 at home depot buy the proper tool, called a stud driver (Gear Wrench part #KDT1708), clamp the stuck nut in the vise, and use the driver to turn the stud. As a Florida redneck mechanic, I find this approach reprehensible, but its the right way to do it. If you go with the driver, assure that the hole for the stud exceeds the diameter of the stud you're putting it on.
Double nutting is for tightly installing the stud in the block. The second nut just has to be on by a few threads. However, the stud does not really need to be tightened into the block. If you can get most of the threads at stud bottom into the block threads by hand, you can put the nut on and torque away. The torque spec is only a proxy for stretching the length of the stud enough to get proper hold down on the head gasket and it doesn't matter whether you are turning the top threads, bottom threads, or both.
Bob