Thinking, especially abstract thinking, is crucial to software development, as often (not always) creating software is abstracting real life into algorithms and data structures. Writing text in a word procesor, notepad, etc. is in my opinion first step to validation of the idea, to having at least faint idea about the complexity of the solution we would like to build.

On the question of "how to think clearly" - I'd say it's pretty individual - some people start "from the bottom", some "from the top" and others "in the middle". Experience is to know which is which and which approach suits you best.