Compilations and organizing files--suggestions

Because of an issue I was having with music disappearing (see these posts if interested):
http://discussions.info.apple.com/webx?128@@.68b7d52c
http://discussions.info.apple.com/webx?128@@.68b45f4b
I went ahead and followed the advice of others and unchecked the "Keep iTunes Music folder organized" to see if it would solve my problem. So for the last week or so things seem to be fine. Nothing magically disappearing. However, now I'm noticing that albums I want to keep as Compilations don't stay organized in my folder on my hard drive. It takes the songs and puts them in the separate artists folders. They show up as compilations in iTunes, which is good, and they stay filed under the appropriate album names, but I'm a bit anal and would like them to stay together on my hard drive as well. Any suggestions as to how to do this? The only thing I can think of is that when I'm importing a cd with multiple artists I make sure that the "Keep organized" is on and then turn it off?
Also, some others have posted that it's wise to uncheck the "Copy files to iTunes music folder..." What's the reason for doing this other than controlling duplicate files? And if you do uncheck that do you have to manually put those new imports into the iTunes music folder?
Any help is appreciated! Thanks!

Given that you can read these files with notepad, I would think you could use Get-Content.
Something like this may work:
$Path = "\\Path\To\Directory"
$12linepath = "\\Path\To\12lineDirectory"
$4linepath = "\\Path\To\4lineDirectory"
$nomatchpath = "\\Path\To\NoMatchDirectory"
$files = Get-ChildItem -Path $Path -Filter *.phy | Select -ExpandProperty FullName
ForEach ($file in $files)
$linecount = (Get-Content $file).count
If($linecount -eq 12)
Move-Item -Path $file -Destination $12linepath
If($linecount -eq 4)
Move-Item -Path $file -Destination $4linepath
else
Move-Item -Path $file -Destination $nomatchpath

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