New to syncing

[Mastiff]

I got some help in another thread, but more weirdness has happened...

I had a bunch of stuff on my player (Cowon D2, looks like USB drive), but I had made tons of fixes to the library, so I wanted to just start over and make everything right. The player had previously been "synced" by dragging and dropping from windows explorer. The D2 contained music/artist/album/songs in a directory structure.

From within MM, I went to the D2 and selected all - remove. I then began selecting entire artists from my library and using "copy to" my D2 (G:/music). I stopped after half the screen was full of copy status bars.

The copy process took literally hours. I started at maybe 8:30, and went to bed around 11:00 with it not even close to half way done. It was done in the morning.

Thing is, all the songs are together under music/. The other folders are there too, presumably left over from before, but all empty. This is not what I want. I'm pretty sure my player uses the folders as boundaries for when to stop playing. Some players also find album art in the folders I think, though mine doesn't.

Anyway. My questions would be, how do I keep my folders intact, and why did the copy take so long? It took maybe 5-10 minutes to copy 4GB in windows explorer. Should I just use explorer and be done with it? It's hard to see the MM benefit for this particular job right now.

Thanks.