<Not a teacher>
You may check out Norman Lewis' 'Word Power Made Easy'. In each chapter, he takes 15/16 related words (e.g. first chapter is about relationship, 2nd chapter is about feelings, 3rd is about psychology etc.), and he will discuss the various usages and also the sources of the words stressing upon the etymology.
I am from India, not a native english speaker. And this book helped me in my college days - when you dont know meaning of a word, you can break the word etymologically and extract the meaning.
About your specific issue, I guess you have to read a lot. If you a read a lot, usages are formed in your mind automatically.