Snafu summary and request for organizational tips from here

Question

Several questions and a long-arse explanation.
Am I stuck with the organizational structure of folders and subfolders I had in mail when I upgraded to Tiger?
If not, how do I organize my mail into folders and subfolders without losing it? (I'm afraid I won't remember to not drop messages into a white one).
I have read in Apple's documentation and here that Mail 2.x does not use the "On My Mac" folder. But when I go to create a new folder (running 2.1), under "location" it says "On my mac," and it gives me no other option. Is this a glitch in my installation, or does the program tell you it's creating mailboxes in a folder it doesn't actually use? Or?
I recently upgraded to Tiger. Late to the party, I know. Last night I also decided to tackle my overflowing inbox (2200 messages). I filed, I organized. I moved stuff around.
Weird stuff ensued.
Some of the messages wouldn't go into certain folders. Huh.
Well, I can fix that; it's probably a permissions issue, or maybe the folder got corrupted in the update. I ran disk utility to repair anything; nada.
I renamed folders. They changed color. That's odd. I went into colors and tried to change them to something else.
I created a new mail folder elsewhere with the same name as the "broken" one and moved the subfolders from the "broken one" into it.
I discovered some of the folders I had moved had nothing in them. I started looking. A LOT of folders had nothing in them, and they weren't in /library/mail, either.
By now you're either banging your heads on your desks or laughing yourself silly at my naivete. (I should point out for your additional amusement that I not only had messages from mail from OS 10.2, I had mailboxes I had imported from Eudora, and one of those was one I'd tried to move to a higher level).
So. I spent several panicked hours trying to fix things, bolluxing them up worse. I finally ended up here, where read very helpful messages, many by David Gimeno Gost. I would like to point out this is the ONLY place I found relevant and helpful info.
Thank you; Thank you; Thank you. I am restored (well, at least my mailboxes are.) Lost two hours of organizational work and I'm back to an inbox of 2200 messages, but I HAVE THEM. (Thanks also to the friends who nagged me until I got an external hard drive and started weekly backups.)
And I'm back to square one with a bulging inbox, only I'm leery about doing anything. If I understand what I'm reading right, unless I like migraines and upset stomaches I:
1. will always have to remember that white folders are simply "scaffolding" for lack of a better term, and cannot hold anything except other folders. Thus I should never try to file messages in a white folder.
2. really shouldn't move folders with subfolders in them at all. Especially if they're from a previous incarnation of Mail, or imported.
3. should never never never accidentally name a folder with the same name, even to "fix" capitalization.
4. avoid renaming folders at all, especially ones that contain other folders.
I realize that's fairly draconian, but I'm often in Mail at 11 p.m. when my brain is dead. Rules that require no thought whatsoever are best. So.
FINALLY, back to my original questions:
Am I stuck with the organizational scheme I had when I upgraded?
If not, how do I REorganize my folders without losing anything?

Answer 1

The “On My Mac” folder has never existed as such, neither in Mail 1.x nor in Mail 2.x. Mail uses that term to differentiate custom mailboxes stored locally on your computer from mailboxes stored on the server of IMAP accounts.
In Mail 1.x such mailboxes appeared in the mailbox list grouped under an “On My Mac” icon, whether that’s how you wanted them to appear or not. In Mail 2.x, this changed to offer greater flexibility in how the user wants his/her custom mailboxes to be organized — see Mail Help’s “My mailbox organization was lost after upgrading Mac OS X” article. This allows the user to have multiple top-level “On My Mac” hierarchies, or name the group differently, or have custom mailboxes appear directly at the top level of the mailbox list for greater convenience, etc.
To answer your question, no, you aren’t stuck with how Mail organizes custom mailboxes, but as you have found out, Mail has some bugs & glitches when it comes to reorganizing mailboxes, and you should make a back up of at least your ~/Library/Mail/ folder before start making changes, just in case.
I sometimes reorganize my own custom mailboxes by renaming and/or moving them, and have never experienced any issues myself, so you should certainly be able to do things like that. There are only two things I recommend not doing in Mail when reorganizing mailboxes:
1. Even though Mail allows it, don’t use a folder as both a mailbox (i.e. to store messages of its own) and as a parent folder for other folders.
2. Never, ever, rename a folder just to change its capitalization. If you want to change from uppercase to lowercase or vice versa, rename the folder to something different first.
A more thorough discussion of these issues, for those who might be interested, can be found in the following thread, for example:
Mail - lost mail - driving me mad