I created a nether portal 5x6 and went through in single player survival. I came out, created a room enclosing it in cobblestone, then went back in only to find it had mad ANOTHER portal about 200 blocks in both the x and z coordinates but the y was the same.
works as intended. Here's a description of how to link your portals properly. I only know the basics of this, so I won't be able to offer advanced help.
For every 8 blocks traveled in the overworld, it will count as 1 block traveled in the nether. It will be easier to do the setup in the nether, since you do not need to move very far.
All portals in this description will be facing in the z direction. Lets say your portal is centered at x=0.0 and z=0.5. Now place another portal centered at x=0.0 and z=4.5.
Next, go to the overworld to x=0.0 and z=0.5. (Not sure if the y value matters.) Build a portal at that spot. Now go over to x=0.0 and z=32.5. Build a second portal here.
Remove any extra nearby portals other than the four mentioned. If done correctly, the portal at (0.0,0.5) in the overworld will link with the portal at (0.0,0.5) in the nether,
and the portal at (0.0,32.5) will link with the portal at (0.0,4.5).
Hope this clears up any confusion.