How to learn programming knowledge scientifically and systematically?

Although not yards, but always have a yard of the heart of the farmers. So always want to learn how to program.

Let's start with your background:
Have graduated several years of engineering male, so the basic knowledge is the University of the rectification of the green Shell C language.
But in addition to the basic variables, arrays, selections, loops, to the pointer that can not remember.

Then because of the job needs, I learned the Linux Shell programming (Linux system basic knowledge is very general), as well as W3school inside HTML, CSS and PHP part of the content.
The knowledge of the database is limited to the underlying SELECET, insert, and update operations.
Finally copied to change to do a functional basis of the site out, work is enough.

Now, want the system to learn programming knowledge, so in Codecademy and Coursera began to learn. The following subjects are completed or in progress:

Coursera:
Learn to Program:the Fundamentals
Computer Science 101
Human-computer Interaction

Codecademy:
HTML Fundamentals
Getting Started with programming
Javascript
Python

Now the problem, it is that I feel that learning is very non-system, meet what catch what.
For example, I installed the eclipse in Ubuntu write Python, but I even the eclipse of the software's nature and working principles are not clear, but also need to go around to find information learning.
I think this way is not scientific and inefficient, so I hope you can teach how to teach self-programming.

As for the final purpose, in fact, I want to be able to achieve a self-developed programmer's level, and even have the ability to change to write code.
Here, there is the problem of knowledge is not the system: I actually do not know what the division of the programmer is.
I'm not sure what the difference between the front and back end of the site is, and I'm not sure what the design is and what is being developed.

As far as I am concerned, my own interest is to do the website, but also to UE, UI design is particularly interested.
Also want to learn the development of mobile phone App.

So I hope you can point out, hope to achieve the above goals, how to do the system of self-study?
What teaching materials can be recommended at the same time?

How to learn programming knowledge scientifically and systematically?