Mail duplicates, storage question

I was in the middle of setting up a new Mail 5.2 backup plan and noticed something odd. I'm using 10.7.3.
I thought Mail since Lion stored mail here: ~/Library/Mail/V2. Sure enough, I have directories there. But they are almost all dated July '11, which I was when I upgraded to Lion. An exception is an account I created recently.
If I go to what I thought was supposed to be the old, no-longer-used directory—~/Library/Mail—there sits my email, with updated files which I presume are new emails.
This, unfortunately, leaves me with lots of duplicates. I don't see them in Mail, of course, but they take up space and I fear could lead to problems down the line. I don't see any way to direct Mail to use the /Mail directory as opposed to  the /Mail/V2 directory.
So: can I just delete the old email directories? I realize there are also other directories with other data, but in /Mail/V2 they also seem outdated and haven't been modified recently. Same with my MailTags info and plists; they are old in the /V2 folder. I can afford to just import or trash the new account that's in there; it's IMAP with few messages. And I have good backups.
And if I do eliminate the V2 folders, do I have recreate a V2 folder with my current mailboxes in it? or can I leave it alone?
Rob

as an update, it does! I've since deleted the accounts but it still looks like there is some stored somewhere on my MBA as the memory is lower than before I started.
Any thoughts? Thank you!

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