Uconnect (and all media players for that matter) do not move or rearrange your files. Each MP3 has header information that includes the artist, title and album. When you insert the SD/USB stick, the radio will scan this header information and build a library of everything on the disk that it can read. This is why it takes awhile to access your music the first time you install the card.
Windows would have done the same thing when you first set up media player. Windows also lets you set tags like genre, composer, mood, etc. Windows only keeps this in its library - the information is not encoded in the actual music file, so uconnect can't read it.
If your files are showing as <unknown>, it is because the information was not encoded when the original music file was created. This is very common if you ever used Napster or any of the other download music sources in the past. It is also common to get the same artist listed with multiple spellings. Different people all over the world did different things. (I've got some songs with tags in German)
If you have a folder named "unknown" when you hit the browse button, then folders it will be because your computer has this same folder. Most likely at some point you imported music from an external device. Windows would have tried to read the album to make a folder for it, but when it was not there it decided to throw it in a folder called unknown.
I've done most of my music saving manually over the years. My PC has a folder called Music. Under that I have a mixture of folders artist and album names. There is also a Misc folder for all of my one off songs gathered from various places over the years. This is exactly how it shows in Folders in the truck, but if I select artist instead - the library will compile all of the songs by that artist regardless of what folder they are physically in on the SD card.
There are editors that let you edit the header information. I went through years ago because it was annoying having the same artist under multiple spellings. I never bothered fixing the album names on the one-off songs, so many of those still show up as unknown. I have not done this in years, but a quick search points me to this one.