I use Musicmatch to listen to my MP3's and have done since about 1998. I have about 20,000, the Majority ripped from CD's, but some have been downloaded.
Because I have so many, I risk getting dupes every now and then (and if I'm downloading from sharing apps I generally download more than one version at a time to allow for lost connections, etc).
Anyway, the main lot are in one folder (my music) but I download to another folder so I can properly tag, check for dupes etc. Once done they go in the main folder.