So now you have done some research in to the water, media and materials for you Aquaponics system to understand how they will work for you.
Now you need to design an aquaponics system. What kind of system? How much space will it take? How will it work? What kind of plants will it grow? What kind of fish will it grow? How many plants? How many fish? How much maintenance will it require? Who will do all this work???
Again take a deep breath. I think many people get all wound up trying to find answers to these questions without having any “framework” for the answers. Start by looking at your own situation and answer a few questions. 1-What is the space available for an Aquaponics system?
2-What do I want from an Aquaponics system?
The goals and situation you are working in should drive the design. Not much point in designing a huge system when all you have is a tiny patio to put it on. And if you have no desire to eat the fish, then don’t go crazy trying to design a system to grow out big edible fish.
If your system will be indoors then you don’t need as much water to handle temperature stability but you will have to deal with lighting. If your system will be outdoors then more water can help with temperatures to a point.
It is often at this point where one should go ahead an build a small system by following a set of instructions to learn and get a feel for handling plumbing and washing gravel. Once such a system is built it will often allow the user to learn about cycling up a system and give many ideas for how they want to build their “real system.” Without some of the hands on experience it can be really hard to know how you really want to do it. There are many “instructions” out there for building a small aquaponics system. I recommend The Barrel-Ponics Manual by Travis W. Hughey 
The Barrel-Ponics Manual by Travis W. Hughey is available free Barrel-ponics Manual
Once you get a sense and feel for doing plumbing and running a small system it will become far easier to know how you really want to do it.
Now my advice here is mostly aimed at media bed aquaponics since it is the lowest maintenance method for backyard use. It might not be optimized for any one thing but it can do most things with minimal effort once set up. In other words, it is the most suited to a variety of things like one would grow in a backyard garden with the least amount of daily effort.
So, figure out your space and goals for the Aquaponics system design, with this information you will be better able to get advice on what to do next.
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