First of all, before deciding how to organize, you need to think about your style and personality. What do I mean by that? Let me give you an example.
My husband is the kind of person who needs to see things. He can't see or find items if they're out of sight. His tools need to be visible. On the other hand, I can't focus if my workspace is cluttered. I need clean empty space, otherwise I find myself unmotivated and overwhelmed. So my tools and projects need a home that is in drawers or cupboards, out of sight.