Complexes are a great way to cut down on logistics costs, dangers to supply freighters and amount of effort required to micromanage your production.
Part 1 - Planning
A station's size determines how much produce it will manufacture. You can determine a station's size by its name. Stations bigger than small will have a size letter code:
Small - most high-tech stations are of that size. Those stations will have x1 yield.
Medium - x2 yield, most stations come in that size.
Large - x5 yield, most stations come in that size.
XL - x10 yield, only solar power plants come in that size.
Knowing a station's yield is useful for planning your complex.
A medium-sized factory can supply with resources 2 small ones or 1 medium one, even though their cycle time and produce per cycle numbers are different.
It's always a good idea to make a list of stations you have placed and still need to place when building a complex, because it can get confusing.
Asteroids have different yield, determining how fast production will go. Yield will not change how much produce you get per resources spent. A basic yield level is 25, and a mine placed on such asteroids will give you 'factory default' values. A level 50 asteroid will be able to produce twice as fast, so, for example, a medium silicon mine placed on a yield 50 asteroid will be able to supply 2 medium crystal fabs instead of one, but will consume twice as much energy at the same time.
PROTIP: you can make closed loop complexes that will supply themselves with energy and all required resources, because solar power plants will give much more energy than their size would suggest. To make a closed loop base you will need a silicon mine, crystal fab, bio fab (argon cattle ranch, bogas factory, etc), food fab (cahoona bakery, bofu, etc) and a solar power plant. Don't forget to take factory sizes and asteroid yields into account when planning!
Part 2 - Advanced Planning
Now that you have a list of factories for your complex you need to think how you are going to arrange them. Take another sheet and draw your complex blueprint. Leave factory squares (circles, ellipses, whatever) blank and fill them in as you place the factories.
A complex can grow quite large, so it's recommended to make it layered, with multiple stations aligned over the y axis. Some basic forms to try out are grids and circles. If it's your first complex you might want to do a 3d grid, as it is simple to plan and expand without worrying about how it will look too much.
Another thing to think of when building your complex is how accessible it will be. It's usually a good idea to put your stations below the eclyptic plane so that ships don't have to maneuver between them, while having the hub on the eclyptic plane to minimize travel time. Mind that your complex hub will aways face north, regardless of how you rotate it before deploying, which means putting it south of a gate your ships are going to be using the most is usually a good idea.
Part 3 - Factory placement
Time to start dropping those stations. You can use your numpad to move and rotate your stations.
4, 8, 6 and 2 are responsible for moving your station along horizontal and vertical coordinates (you can switch your vertical coordinates by pressing insert)
1, 7, 9 and 3 are responsible for rotating your stations. In 9 cases out of 18 it will only add to confusion and make your complex look more bizarre than it needs to.
5 allows you to center your station on the closest object. Very useful if you want to have perfect intervals between your stations.
When you are satisfied with your staion's placement press enter to drop your station. I recommend you put your stations below the ecliptic to make navigating your systems easier.
You can use a tractor beam to move stations and mines. Moving stations is quite easy, but you probably wouldn't need to do it very often because you can place them wherever you like. Mines, however, are a different matter. You will have to move them most of the time (unless you build your complex around that juicy asteroid) and you will hate the experience. In 9 out of 10 tries your mine will start spinning when being towed, resulting in your ship loosing the "grip" on it. You should note the axis around which it turns and shoot your beem there. It's also useful to limit your speed to about 30m/s before the mine stedies itself and you are sure it will hold.
If you are going to add mines to your complex you may want to move them in place first so that the stations don't get in the way.
Another thing to be aware of is that the mines are so large, that if their docking facilities are pointing away from the hub they may very well be outside the complex range. You will learn how to overcome this obstacle later in the guide, but it's best to simply avoid it by rotating the mine to face the complex.
PROTIP: A safe distance to put between stations is 2 km (along x-, y- and z-axis) for most stations, however, if you are going to place huge stations like a solar power plant xl you may want to make it 4 km or even place them separately from the main complex body.
PROTIP: After you've placed your factories, check their shields to make sure that they don't collide, as it will eventually lead to destruction of both your stations and all connections between them, as well as any ships docked at the complex hub. The best way to check their shields is to press "Enter" in the sector view so you will see the precise numbers instead of a small colored bar. If their shields are below 100% you've done somethng wrong.
Part 4 - Connecting stations into a complex
You will need n - 1 (where n is the number of stations) complex constructions kit to construct a complex.
First, connect 2 stations that are going to be closest to your complex hub, so you have more freedom in placing it. Then, connect your other stations to your hub. This part should be very straightforward if you've done everything correctly in the previous steps.
To make sure your complex runs smoothly you should let your stations build up a small stock of their produce before connecting stations that will use it as resources. Stations and complexes will flash white if they don't have 100% of resources required to start the next cycle. You should make sure that is not going to happen so that white flashing will notify you of real problems only.
Stations can be connected if they are within reasonable distance (about 15 km).
PROTIP: If your stations are too far from the hub to be connected you can make a secondary hub, which will then be connected to your main hub. To do that, connect 2 of your outlying stations and put your secondary hub as close to the primary hub as possible. Then, connect your primary hub to the secondary hub with an additional complex construction kit (The first hub to be chosen for connection will remain, the other will disappear).
Part 5 - Conclusion
You now should have a working complex. Assign freighers to bring in resources (or bring initial crystals/energy cells if your complex is a closed loop) and set its settings much like with any other station.
Before you set up your stations I recomend using a complex calculator.