To put a portal in a specific place, look in the bottom right corner of the map. There will be four sets of numbers. X, Y, Z, and YAW. Go to where you want the portal, and look directly at the ground. Put your mouse in the center of the screen and record the coordinates of a piece of paper, or remember them. Some of the number may be "40, 596.78" and that won't fit. What I do is round it, making it 40, 597. Yaw is usually a small number like 75.48, so you can do the full number there.
Hope I helped...