and I am wondering if wav is really better than FLAC...
FLAC, ALAC, and other "lossless" formats are losslessly compressed. This means that the audio data is identical to uncompressed formats such as WAV and AIFF when decoded, but you can save ~50% disk space with these formats due to the compression. (think of them like ZIP files for audio) This is also useful when storing files on portable devices, or accessing the files via a networked device.
WAV typically has poor metadata/tagging support, so AIFF is preferred as an uncompressed format, but generally FLAC or ALAC are the most popular formats to use, and both have very good metadata support.
As for how classical music is tagged, I still haven't quite decided on everything yet, but I generally put the Conductor in the Artist field.
I'm not sure which of my tags are custom ones now, but for classical music, I am also using:
Composer, Composition, Composition Name, Conductor, Movement, Opus #, and Orchestra tags.
An example might be:
Composer: Ludvig van Beethoven
Composition: Symphony № 3 in E-flat major
Composition Name: Eroica
Conductor: Herbert von Karajan
Movement: 2
Name: Marcia funebre: Adagio assai
Opus #: 55
Orchestra: Berliner Philharmoniker
I then have expressions set up to display this as: Ludwig van Beethoven, Symphony № 3 in E-flat major, Op. 55 “Eroica” ‒ Ⅱ. Marcia funebre: Adagio assai
One of my classical views is set up to group by composer, then composition, rather than albums.
Media Center doesn't care about your file structure, so that doesn't actually matter. And as long as the files are imported in Media Center's library, there is a very powerful renaming tool that will rearrange where your files are located on the disk with ease.
The advantage of splitting out all this information into separate fields, rather than simply filling out the track name as "Symphony № 3 in E-flat major, Op. 55 “Eroica” ‒ Ⅱ. Marcia funebre: Adagio assai" is that I can omit many of these fields from the filename to avoid running into the 260 character limit.