The best practices are the ones that fit you, and they incrementally evolve as you evolve making all kinds of discoveries.
When you find your workflows and organization becoming unwieldy, then you'll know you need to change something. (Change when it "costs", in whatever way imaginable, too much not to change.)
So keep doing what you are doing, but find little moments to read about features in TiddlyWiki, about plugins, about all things information/knowledge/documentation management.
Take all that you read and park each in the back of your mind, so that when you do run into things getting unwieldy, you'll have a "wait a minute, I read something about that", if not enough for you to know what to do, you'll know enough to ask the kinds of questions that get you help right pronto.