WAV file

WAV files actually do not support metadata. The data that is associated with them in iTunes is a direct function of the iTunes software, as I understand it. So if you copy via drag-and-drop all the associated data will be lost. This is a huge disadvantage to ripping in WAV. The only way I know of to avoid it is to have iTunes move the files from within the program. You can use the "Consolidate Library" command to do this. Go to the Advanced menu and change the location of your library to the target drive. Once the target drive has been set choose "Consolidate Library" command (File>Library>Consolidate Library). This will move a copy of your entire library to the new iTunes music folder that you've chosen as the target, while leaving the original copy in tact. I'm pretty sure that's the only way to do it, but anyone feel free to correct me if I'm wrong. You can avoid this problem in the future by ripping to Apple Lossless or AIFF, both of which actually do support metadata as I understand it.

Try copy and paste instead of drag and drop.

My understanding is this: the itunes library is a database and it has a path for each song. The path tells it which folder it is in - or which folder within a folder within a folder. As long as all your "moving operations" are within itunes, the itune libary keeps track of where each file is. It is the library that contains the tag, not the actual song. Itunes links the tag in the library with the path of the song to keep a tag associated with a song.

If you are using an external hard drive for your original ripped music files, great. All you need to do is make a duplicate copy of that hard drive - meaning preserving the folder structure - on your backup hard drive. You might call your primary hard driver "Music-1" and your backup hard drive "Music-2". If Music-1 ever crashed, you could just rename Music-2 to Music-1, and itunes wouldn't know the difference. It would still be looking at an external hard drive called (renamed) Music-1, and all the music files would be in place within the exact same folder structure, because you carefully made sure that the two hard drives had the same folder structures. However, if yu let itunes move things around on Music-1 without making the same structural changes on Music-2, the paths in the library would not correspond to Music-2, and if Music-1 went down, itunes would no longer be able to associate the defunct paths to songs with the tags.

You should also backup your library file, along with your music files. You can do it somewhere on Music-2.

As Jax2 stated, I ran into the same thing, so I am now using no compression but am ripping into WMA files rather than wave.
Only other option is to use Roxio release 6 or 7 which allows you to rip in WAV files and rename the files before ripping them. tedious but it works.

AIFF is like .Wav in every way except it supports tags. .Wav is not really a workable format for long term archiving because of the lack of tags. You can preserve the metadata for .wav files in iTunes by using the export library function and then reimporting the library file to the new installation. Keep the files in the same basic as the original but I have found the drive letter need not be exactly the same.

If EAC has a function that will tag .wav files with ID3 tags but I am not sure how universally supported this is.

For archiving, you want two things. You want a bit perfect copy of the sound file itself with no compression at all. But you also want complete and accurate metadata for each file so you actually have a file that you will be able to use with various applications for many years. .Wav just does not fit the bill.

I meant to say same basic directory structure as the original. Keep it simple, i.e., C:/iTunes/ or C:/documents/mymusic/iTunes or whatever.

I have found the best solution is to keep a drive that is totally separate from you system disc just for mass storage of files. On that disc, every few days or every week export your iTunes library to a file in the root of the drive to keep it updated. If something goes wrong on your system and you need to reformat or whatever, you have everything you need to restore your library, including the .wav files.