Echoes a lot of mine. I would also endorse use of replicants and importing over indexing. I used to index but always worried that the link would break.
DT3 works best when you have separate databases for separate projects but those projects are in themselves comprehensive. The more detailed and thorough and structured the more useful it is as an adjunct brain. I’ve found that the structure evolved over time, and my initial forays were eventually remapped as research progressed. Paralleling understanding in a way, but don’t worry about that, get in there and stick with it. It can take a while, even years, but it’s really worth it.
There’s other tools, like the supercharged mind mapping tool Tinderbox, which can link to items in DT3 and set up other views and ways of interacting. The rather marvellous Beck Tench demonstrates a detailed use of this over a series of videos https://m.youtube.com/watch?v=IOWLOMGFAEw