I could have be more clear - apologies
Basically, DTPO is not technically involved in the filing and organisation of my PDFs but it is directly involved in searching them. I make use of the ‘synchronization’ feature. Let me explain.
Completely outside of DTPO, all of my work is contained under one single MAIN folder, within which I have multiple other folders, such as WORK, TEACHING, ADMIN, CONFERENCES, PUBLICATIONS, LECTURES (RECORDINGS), RESEARCH and ADVISING. Again, this is on my hard drive, not in DTPO. Within the RESEARCH folder, I have a folder called ‘JOURNAL ARTICLES’ and naturally quite few others (e.g., broad topics of central research interests). That JOURNAL ARTICLES folder holds all my journal articles, organised by journal title. It’s just under 800MB in size and has 1750 items, so it isn’t that small. When I download a pdf, it gets put into the appropriate journal title folder within the JOURNAL ARTICLES folder on my hard drive, not in DTPO.
But here’s where DTPO comes in.
Within DTPO I have a folder off the root called ‘MAIN’ which I use to synchronise with the MAIN folder I mentioned above. I do this by highlighting that MAIN folder in DTPO and then using the keyboard shortcut OPTION+COMMAND+S (also in the File menu) to synchronize the contents. As I understand it, this doesn’t actually import the content of the MAIN folder on my hard drive (I wouldn’t want it to), but rather indexes it. Someone do correct me if I’m wrong on this. Anyway, I do this perhaps once a day, usually in the morning, or even during the day if I have added a bunch of new journal articles or other content to the MAIN folder on my hard drive.
This way, everything that is in my MAIN folder on my hard drive is actually accessible via DTPO but not held by DTPO. And of course this means that it is fully searchable, including the contents of those 1750 journal articles. As I am writing, I can search within that JOURNAL ARTICLES folder because, as you know, you can specify where you want DTPO to search.
It’s a system that works really well for me, but would love to hear examples from others.