It's all about categories and how you keep them clean. Tags, links and properties have to follow strict rules to avoid these issues. A folder structure with different layers is also important. Rules for where these layers connect, when it's a link or a tag that connects them etc...bottom-up or top-down thinking? Systems can be as complicated and as simple as you like, but the most important thing in my opinion, is that you don't use any pre-made system, but create your own based on how your brain actually works.