Let's see if I can help any one this one:
I have Twonky's Video Tree set like this:
Video Node 1 - Folder
Video Node 2 - Date Added (2 points off of that - year & date)
Navigation Tree Setup - Custom
I have 4 storage drives. All drives have the subfolders directly in the root. When I added them to the sharing, I just added the roots (n:\, o:\, etc).
When browsing by folder, I get something like this:
Twonky "merges" folders with the same name, so I only see each category once, but with all videos inside of them. I also have some of the categories broken down, such as tv shows/series type of deal, and they show up perfect.