I haven’t yet discovered the ideal system for internal organization. I’ve tried some things based on the Library of Congress system, the Dewey Decimal system, and others, but it’s all ultimately arbitrary. You can make it as vague as you want or as specific as you want, but ultimately, it’s going to be a compromise. There’s not much you can do about it.
Tagging (and eventually key-value metadata, hopefully) and smart groups are, IMHO, the best way to minimize the artificial and arbitrary folder hierarchy metaphor. If you want to work in a particular area, summon the relevant documents with a smart group, and go from there. Of course, this depends on a certain behavior, namely that you don’t just dump things into DTP.
There are different usage scenarios, and it’s important to realize that. Bill DeVille represents one particular philosophy about DEVONthink. From what I can tell, it’s by far the prevailing philosophy. And Bill DeVille is extremely intelligent, educated, knows what he’s doing, and does it well. I can’t criticize what he does or how he does it, and his advice is impeccable. All I can say is that his philosophy doesn’t work for me… but, fortunately, DTP doesn’t force one to work that way.
I don’t use DEVONthink as a general document storage system. That’s what the filesystem is for, as far as I’m concerned. I tried shoving all of my documents into DTP databases and, well, it was absolutely ridiculous. I have thousands of books and hundreds of thousands of other documents in PDF format, and if I need to find a particular one I use Spotlight. Even one database for each discipline (History, or Philosophy, or Psychology, or Religion) would be untenable, and the benefits of having DTP manage the information would disappear, even as well as DTP scales.
Essentially, where Bill and I differ (and he may have different thoughts on this – this is just my impression) is that he views DTP as a warehouse, and he relies upon DTP to do warehousing work. He stores documents and pieces of documents, takes inventory, and expects to be able to find the information quickly when he needs it. He also enjoys the connections DTP makes between different documents. The warehouse gets more full over time, but that just makes Bill’s setup function better. As far as I can tell, this is what DTP was intended to accomplish.
I view DTP as a refinery. I bring in raw material (books, articles, other documents), I process it, creating new documents from the distilled and purified essence of the raw material, and then I throw that raw material out. I know every word of my database, because I wrote every word of it.
So my databases are almost always far smaller than Bill DeVille’s. The content is almost always RTF files, not PDFs. I rely much more heavily on properly naming, tagging, categorizing, and describing documents. I rarely (if ever) use “See also” or certain other of the tools provided by DEVONthink’s artificial intelligence – because I have always prided myself on my ability to see patterns and draw connections between disparate phenomena, and at least with my databases I haven’t seen compelling genius from DTP’s implementations.
Those are two different ways of using DTP, and they’re quite different. The extreme ends of one spectrum. There are probably other spectra, and Bill and I definitely do share some strategies in common… but anyway, since you’re a new user, I wanted to express my opinion clearly: There’s no “right” way to use DTP, and it’s a very versatile and powerful program, and you should just concentrate on what works for you.