How do I properly manage audio files with iTunes?

Hello Dear Readers,
I am going to start using iTunes exclusively for my music collection management. Previously, I had only used iTunes for managing content for my iPhone 4. Now, I am wanting to import all of my media (music) files into iTunes for general use and playback.
For example, I have over 3,000 music files, and I would like to know the best way to get them into iTunes. From a lynda.com training video about using iTunes, I learned that there is a folder called "Automatically Add to iTunes", which is monitored by iTunes for new files to import into the iTunes library. However, I would like to know if this is the *best* way to do this. For example, can I just*move* my 3,000 music files into this 'Automatically Add' folder and then let iTunes do its thing?
Will iTunes *move*the files that it is able to manage OUT of this folder and into one of its managed folders, such that there would be no duplicate file left behind? Is it correct in saying that the files that are left in this folder that were not able to be handled by iTunes and must be handled differently before they can be imported into iTunes. Or is there just an all around different, and better, way to get these music files into iTunes? Thanks for your advice and opinions!
There is also the issue of what to do with the commercial CDs I have (less than 50). I would like to discard these and just maintain them on digital form, e.g., my 2 TB hard drive. However, I am getting varying opinions as to how to do this. I need 2 things: 1) to archive the CDs for retrieval later in case I need the songs that are on them, and 2) MP3 versions of the audio CD files for use on my flash drive which plays on my car audio system. These would also be the files that I manage in iTunes.
Some people have suggested using Exact Audio Copy to make a FLAC and a LAME MP3 copy of myCDs. Others have suggested keeping an ISO copy of the compact discs for reference archive. Personally, I am wondering if I should just import my commercial CDs directly into iTunes, and then pay Apple $25 annually to maintain copies of these, as announced by Steve Jobs at the WWDC that this cloud functionality was forthcoming.
I am in need of some informed, educated opinions and suggestions as to how I should proceed.
Then, there is also the naming convention of the files. When the files get ripped from CD, I can add the freedb information to them for the ID3 tagging. However, I need to know how to specify in what system that the file names are comprised. This is what I am thinking of as my folder and file name format, at this point.
For the naming scheme of the audio files, I am proposing the following:
For most music by 1 artist on a disc, I would do as follows:
Folder Name: AlbumArtist - Album Title (year)
File Names: Track number (from 1 on up, with NO leading zeros) Track Title
For compilations with various artists, I would use the following for the schema:
Folder Name: VariousArtists (album artist) - Album Title (year)
File Names: Track number (1 on up) Track Title - Track Artist.
Do these seem like reasonable naming schemes that would be good for using on all audio software and equipment, such as my iPhone, my car audio flash drive player, and in iTunes?
I know that this is a lot to ask, but I am just trying to learn how to do things correctly and most efficiently so that I don't have problems down the road with my iTunes library. I welcome input, discussion and of course, dissent! Thanks!
~Antonio

how do you do it with itunes 11???
it is really frustrating me!!

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I have over 3,000 music files, and I would like to know the best way to get them into iTunes. From a lynda.com training video about using iTunes, I learned that there is a folder called "Automatically Add to iTunes", which is monitored by iTunes for new files to import into the iTunes library. However, I would like to know if this is the *best* way to do this. For example, can I just *move* my 3,000 music files into this 'Automatically Add to iTunes' folder and then let iTunes do its thing?
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Hello tt2,
I have given this a lot of thought and attention over the last few days. As well, I appreciate very much your input and offers of help.
The major 'problem' that I have is that the files are most definitely not consistently named. For example, they include the likes of the following:
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And these are only examples, based on my trying to get across how variant the names are. The actual file names are far more wildly various than even these, seemingly consistent file names.
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