This is how it works:
Every time you enter a portal, the game looks for an exit portal inside +/-128 blocks square (y is irrelevant). If you enter a portal at x=100, y=60, z=200 in the overworld, this corresponds to x=12, y=60, z=25 in the Nether. The game scans a square from (x=-116, z=103) to (x=140, z=153), for all y values from 0 to 128. The closest portal in that space is where you appear. If there is no portal in that area, one will be created in a suitable place. Since there is a chance the x=12, y=60, z=25 will be obstructed, the game will search for an open space in that +/-128 blocks square. If such space is found nearby, all will be good, the new portal will lead back to the same one in the overworld.
Note that the game will only scan within the map height. That means that if you place a portal above the nether ceiling, it won't be found, and the game will create a new one for you.
However, sometimes the game will put the Nether portal far from the starting point, if it can't find other suitable place. Let's say it puts the Nether portal at x=80, y=60, z=110 (this is still in the +/-128 bounding box). When you enter that portal the game will search the corresponding space in the overworld: starting from x=640, z=880, it will search the +/-128 blocks - from x=512, z=752 to x=768, z=1008. As you may notice, the original overworld portal is well outside this box. So the game will create a new portal in the overworld. This is what is happening in your world.
To fix that, write down the coordinates of the portal in the overworld (use F3 to get them) and divide them by 8. Enter the Nether, go to the calculated coordinates and create a portal from the Nether. You don't have to be exact, as long as you are within 16 blocks from the calculated coordinates (you need to match only x and z, y is irrelevant). Then the game should find the original overworld portal. Or: Move the overworld portal using the above logic.
In described situation, there is no way to make the two portals lead to each other without moving either of them. I'd move the nether portal and if the new position is outside of the fortress, I'd build a short safe walkway to the fortress.
Here is a crude drawing of the process: 
It's probably not worth it to try to create some intricate, custom designed mob trap for both spawners. I would only focus on one, how many blaze rods could you possibly need? Unless, of course, you want to create an intricate, custom designed mob trap. I don't think anyone can help you on that, though, because I've never seen it done before (although I could be wrong). Whatever you choose, good luck!
Best Answer
The Bounding Box Outline mod will show you nicely-shaded bounding boxes for all Structure Pieces placed in the world, including Nether Fortresses. It's currently available for 1.6.x and requires Minecraft Forge.
I've already got a Forge profile laying around, so it was a simple matter of dropping the mod in a fresh game directory along with the Skyblock 2.1 save, an edit to the
level.datto enable Creative, and lo and behold:So yes, there are two Nether Fortress "ghosts" not far from the glowstone island.
The nearest corner of the one visible on the left is at approximately 76, 62, -63 (XYZ) and stretches to the North and a bit to the East from there, not including a hallway protruding to the West (the direction back toward the portal, but farther North than this corner).
The nearest corner of the one visible on the right is at approximately 94, 71, 73 and stretches East from there with a Southward and downward tendency.
You could go off those numbers and just grope around trying to make a blaze-spawnable area without the mod. If you want to use the mod though, it's quite easy to install starting from zero modding experience: download and use the automatic Forge installer which will create a new forge-enabled Profile, then drop the Bounding Box Outline mod's zipfile into the new
.minecraft/mods/folder that will be created after you run Forge once. Once in the game, turn the mod's visuals on by pressing F3+n (simultaneously) and the fortresses will show up bright as day.