Indexing and Importing, retaining org. fold. struct. for ftp

So I have searched through the forums to find an answer to this question, as similar “indexing vs. importing” threads are ever so common. Unfortunately, I didn’t find exactly what I was looking for.

I will post my questions below, but I start by saying in alternative resolutions to these problems (there is probably a lot I have not considered) would be appreciated.

I host an FTP server on a NAS that serves my huge conglomerate of files. However, I enjoy using Devonthink as my primary file manager. Many times I clip things from the interent, copy web pages as PDFs. These types of files don’t really bother me if they make or not into the folder structure. On the other hand, I am shuffling files around in DevonThink and changing folder names when a better organization method comes to mind.

  1. What is the best solution to retaining an outside folder structure so it can be accessible to FTP & it’s users. And is there any way to do this that it mimics the look of my revised folder structure in devonthink.

  2. Is there any alternative ways I can organize my system to accomplish these tasks?