...After a timeout I'm back, and refined my complex construction techniques even further than before., so, I figured it was time to release a version two of Complex Construction for Dummies - with less annoying verboseness and more easy to follow stepness
Complex Construction
Node Theory
Before you can start plonking down stations and making them look really darn pretty, you need to know the logic behind how they fit together. The key to all this are the port nodes. They are easily identifiable on a station and look something like this:
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These nodes are the bits the tubes connect to. When two stations are connected it will find the two nearest nodes on each station, and then place a "long" tube piece from each facing directly outward, next, it'll attempt to join these two pieces by placing one or more pieces of variable length. But we're going to cheat, and place the nodes so close together, all 3 pieces will fold atop each other and look like a single thick piece of tunnel.

This little lesson is the key to all the next steps and how you'll make your complexes look like you probably envisioned when you first heard the word "complex"
Quick reference:
Keypad 7, 9 - Rotate station around horizontal
Keypad 1, 3 - Rotate station around verticle
Insert - Switch between horiztonal/verticle map mode
Plus, Minus - Zoom camera in/out
F1 - Cockpit view
F2 - Exterior view (Front/Back toggle)
F3 - Target exterior view
Before we start: Placing your first station
Placing your first station should be pretty easy, stick it wherever you like basiclly; it does help to remember the scale of the map, some very large sectors (ie. Mists of Elysium, Ministry of Finance) it's very easy to stick a station miles from any other stations by accident because you didn't consider how BIG the sector was. To illustrate, It's quicker to fly from Great Reef south gate, to West Gate Resevoir of Tranquility than it is to go halfway across Mists of Elysium.
Step 1: Adding another station
This is the real meat of it, everything else is fluff. Over the months of playing I've come up with a foolproof sequence to do this quickly and effectivly, so each step is relativly small. First thing, get into a smallish craft (Anything but a capital ship really), fly over to the station to connect to, and target it directly (The station itself, not the hub complex)
Step 2: Positioning yourself
Now, search the station for the node you want the other station to connect to, fly about til your find it. Now, fly up to it physically so you are pointing nose-toward the node, use your lateral thrusters (strafe) to position yourself as close to perfectly dead center and level as you can.
Sort of like this, but with your HUD turned on
Step 3: Camera one...
Press "F2" twice (by default), this'll give you an external view face-toward your ship, press hard left or right on the control and swing you ship around 180 degrees so your back is now facing the node. This means we are now "seeing" the direction the node does.
Back to back they faced each other... or something
Step 4: Camera two...
Next, press "F3" - (You did select the station right in step 1?), and you'll now have an outside view of the station. Press "up" or "down" on the keypad (or PoV hat by default on joysticks) to bring the camera either directly above, or directly below the station. Directly below is usually easiest.
We are now ready to position the station
Step 5: To me, to you!
Now, get out the station you wish to place from your TL, scroll it over to existing station, when it's close press "5" on the keypad and it should jump to the same location.
Step 6: We control the horizontal...
Have a good look at the station you wish to place (rotating the station (7, 9, 1 and 3 on the keypad) and zooming the view (+ and - on the keypad) should help you locate the nodes if unsure).
Once you have found the node on the new station to connect to, rotate the station until the 2 nodes appear to facing each other precisely - using a straight edged object like a pen or piece of paper will help. And move it until they're close enough for your personal taste; closer the better in my opinion - Just make sure they do not physically overlap!
Step 7: ...and the verticle
So the stations are neatly lined up, neat, but nothing new from my old tutorial. Here comes the clever part... remember we spent all that time positioning your own spaceship? Press F1 to return to the in-cockpit view.
Next, press "insert" on the keyboard to go to the verticle controls, your ship is the same height and angle as the node remember, now you can use the up/down and rotational controls to match the height of the node so both nodes are looking precisely at one another.

Try see past the console to the node behind it
Finally, when you're happy, place the station, and then place your complex kit, don't worry about order too much it'll use the closest nodes, which thanks to you are VERY close.
See how close these nodes are?
Using this system, you can even position stations at angles
One off step The hub
Obviously each complex will have one hub. The hub is a little different in so far it doesn't like being squeezed up to another station, place it too close and it'll place itself god-knows-where and look horrible. Do the same process as you did for the other station, but place it at least one and a half times the width of the station away from the rest of the complex, so that you can get 2 and a bit long tunnel pieces in (one from the hub, one from the station and a teeny one in between)
Also in older versions of X3, the hub ALWAYS places itself due north, I havn't tested if that's true in the latest patch since my home sector faces north anyway.
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The Last Word
Some final stuff to keep in mind is:
- Don't let two stations come physically into contact or they will "collide" causing shield drain, CPU and loading lag (sound files etc), and potentially be destroyed.
- Because you are facing the direction of the node, it's possible to place stations at angle to each other

- ALWAYS use the same complex kit type each time (if you bought from the Boron, buy your next kit from them), if you change kit type, the hub will jump randomly.
And there you have it! - Go forth and create obscenely large framerate murdering complexes!