This is a problem with all those that prefer a classic WYSIWYG editor, where you have buttons to do formatting (like me) and markdown is invisible in the background. There’s a thread on a such editor, it will be done in the near future. Here’s the thread: A Typora-like editing mode (edit and preview at the same time)
I don’t know anything about the Zettelkasten method, sorry. I worked on implementing my own system, aiming at the simplest organisation at the top level structure. So basically, I have two folders at the top level: INPUT and OUTPUT. Input is everything I read or collect as information, OUTPUT is where I create stuff (documents, articles, etc.). OUTPUT draws upon links and information from INPUT in any way possible or fitting.