I want to know the structure and whole picture of scientic methods or
approaches. To develop or create things and systems, we use
theories,methods,methodologies,procedures,standards,mauals,etc.I want
know if someone definds thoese words and interrelation or hierarchy of
them. I often find people misuse method as manual in vain.

Your answers will be found in Thoms Kuhn's 1962 landmark book: The
Structure of Scientific Revolutions.  Kuhn was first to use the word
"paradigm" in this context.  Your use of language in the way you ask
your question, suggests that you may be surprised to discover (as I
was) that the "hierarchy" at work is not rigid, rather it is dynamic. 
This is the "essential tension" in how a scientific method or approach
(a paradigm) is accepted into the mainstream.  Enjoy.