From reading related threads on AgoN, I gather that many of us are happy storing our music as Apple Lossless files, because we can't hear any difference between AL and WAV or AIFF. Also, John Atkinson in Stereophile examined files that were converted into AL and then converted back to lossless format and found that the result was a bit perfect copy of the original (article can be found by searching stereophile.com). So, there is analytical reassurance, if that helps.
BTW, Apple Lossless files can be converted to WAV files, but there's not much point to it. If one is persuaded that AL is truly lossless, there's no reason to go back to larger files. If one is not, then the reconverted WAV files wouldn't be as good as the originals, so why would you want them?
Kubla, I use iTunes on Macs, so can't address most of your questions. But with respect to compilations, check to see that the "part of a compilation" box is checked in the file's Get Info window. iTunes always stores by artist, except if this box is checked. Then it stores by album title inside a folder called "Compilations."
BTW, Apple Lossless files can be converted to WAV files, but there's not much point to it. If one is persuaded that AL is truly lossless, there's no reason to go back to larger files. If one is not, then the reconverted WAV files wouldn't be as good as the originals, so why would you want them?
Kubla, I use iTunes on Macs, so can't address most of your questions. But with respect to compilations, check to see that the "part of a compilation" box is checked in the file's Get Info window. iTunes always stores by artist, except if this box is checked. Then it stores by album title inside a folder called "Compilations."