In response to your first question: It's not a bad thing to learn php and javascript together because they have a very similar syntax, but you should understand their purpose. PHP is used for server side scripting ( so accessing databases, processing information from forms and such), and JavaScript is to make html more functional. The big thing about javascript is that you can create dynamic web pages and such.
Your second question: I am by no means an expert on this matter because I have received no professional education on it, but what I usually do to organize my code structure before hand is to map it out on paper. You want to start out by writing a short paragraph that will describe what the program does. Then you will want to start outlining certain functions that you know you will need to make, and jot down what they are supposed to do and maybe, if you can, you can sort of diagram the algorithm used in the function you want to make.
Now, you will notice that you almost always will think of extra things while you are coding, but doing this will help you get started with the project and you will know what to expect and what to look into.
As for education through books: You will only learn from the books by reading little bits of it and then practicing that concept. Even though the book will be divided into chapters, you will most likely not want to read a whole chapter at a time. You will want to take it two to three pages at a time a day and then use those concepts to make programs. It will take you some time, but it won't be boring if you are applying the ideas to cool projects. In my experience, I liked this method because I would learn something new everyday, and since I would learn it little by little, it stuck a lot more in my mind.
As for some project ideas, you might not want to start doing like fps game related projects, but you can make some console games like tic tac toe, battleship, and a number guesser. You could even make your own mmo and that will give you good practice with the concept of functions and loops.
Good luck, and if you ever need anything please make a thread here, we are always happy to help people who are giving effort.