1) How do you deal with songs that have multiple genres?
In "Singles" I sometimes copy individual MP3's into both Rock and Metal. It comes up less often than you'd think.
2) how do you deal with album that has songs of varying styles?
I just pick the one genre that makes the most sense. As long as I know, or can quickly find which genre an artist is in, that's what matters. How long does it really take to check if I put an AC/DC album in Rock, or Metal?
3) Compilations
I either place it in /Albums/Soundtracks (if it's a soundtrack), or make a "Various Artists" directory in /Albums/Electronic or whichever genre makes sense. Almost all of my compilations are dance or electronic music.
4) I don't understand how you handle singles.... To me it looks like your singles folder is intended for random songs, not to handle actual CDS/CDM style singles
I actually removed most of the EP's and CDS rips from my MP3 collection because I found I never listened to them. I would take the individual MP3's that I really liked and placed those into my /Singles/ directories. Otherwise I could treat them just like I do my Albums.