Also, it seems to have a limit to the number of files it can see in any one folder, including the root directory. However, if it doesn't see anything, it's probably just not compatible. When I found a drive that worked, I had to piddle with the organization or it only saw 1000 files.
I ended up organizing mine into folders for each artist, then folders under each of those for each album. But I have a lot of full albums. If you have a lot of single tracks from albums, or don't care whether full albums play in order at the same time, you could just do it by artist.
EDIT: Or you could just make a bunch of folders and dump less than 1000 files in each. Also, I created a playlist (an .m3u) in the root directory to make sure it saw everything. Don't remember whether that was the thing that eventually got mine seeing everything or not.)
Keep in mind, I have the uConnect 3.0 (the baby/base one). Not sure how much of this will apply to the higher-end ones.