IMAP Gmail & Apple Mail: Organizing Emails

I’ve just switched from POP to IMAP on Mail.app in an effort to synch my iPhone and my Mail.app. I followed the step-by-step instructions on Gmail’s support page. I’ve got a few questions . . .
1) What’s the best way to organize the thousands of emails archived in the new All Mail Folder? I’d like to create basic folders (i.e. Work, Family, School) to sort my emails.
2) Can I use the Apple’s “Sent” Folder (the one with the paper plane icon) to view all of my sent emaisl? Or will my history of sent emails forever be stored in the Gmail “Sent” subfolder?
Thanks.

Sorry, I just noticed something. The problem is not only with the mail that comes in from the Fetch accounts. It also happens with mail sent to Gmail.
In the left-hand column of Mail 3.0, there's a folder called "Gmail" with a triangle next to it. Let's say a new mail comes into my inbox to my Gmail address. If I click on it in the inbox, it gets marked as unread in the inbox. However, I still see a "1" next to the Gmail folder indicating there's an unread message. If I click on the triangle to expand the folder, and then click on "All Mail", the folder seems to "update" itself and the unread email is marked as read (without me clicking on the actual message).
Otherwise, it seems to stay marked unread. Why is this?

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