This is the part that keeps me - as a new and mostly-thrilled DT user - up at night. I am really trying to just use DT to index files. I prefer to keep one instance of a file, and have that instance be in my main directory.
However, in practice, it’s increasingly hard to not simply import files. I’m pretty careful about maintaining one instance of any file I’m likely to edit (eg, Word), but some reference PDFs have slipped in.
When I look into the pkg, and see all the original files organized by type, in folders “0”, “1”, “2”… “f”, I start to worry.
If / when the days comes that I move out of DT, it will be a nightmare to get all files out and properly organized. I’ve already got much in there, after only a couple months. Years from now, it will be thousands…
And, frankly, it’s more a matter of when than if. I’ve been around long enough to assume that someday all programs will stop being supported, or that I will stop using them. I know that DT has been around a long time and has a great track record (one of the reasons I finally chose it), but still - life is long and software is young.
This isn’t to scare you, @Brian_B, but just be cautious. Sorry to take your question on a slight tangent, but I think it’s relevant. 
One thing I found helpful in answering your question (and many others): the free ebook Take Control of DEVONthink 3 by Joe Kissell. I found it to be invaluable in getting started. He explains all the parts and concepts of DT very well, including all the ways to handle your files. I still refer to it, months in. It’s linked here somewhere on DT’s site. Check it out!
And if anyone else has any tips on file management in DT, for us newbies, I’d appreciate it too!