Smart Mail Folders and Rules in Mail

Q. I’m trying to set a Rule in Mail to organize my messages. I made a Smart Folder to sort my messages but when I deleted them from my Inbox they were deleted from the Smart Folder as well. Can you tell me what’s wrong?

A. To begin with a Smart Folder in Mail is actually a special way of viewing all of your messages. Like a rule or a filter you can specify the criteria that picks the the messages out. For instance a Smart Folder will gather all the messages to and from an email address or domain that you specify.
Many users organize the email they want to save in folders – a Smart Folder will gather all the messages from all of the folders in your Mail application. You can even choose to include you Sent messages. It does this without moving the messages. So if you delete a message and then empty Mail’s trash you will delete the message.
If you want to keep a message in an organized way then you should create a folder or Mailbox as they are called in Apple’s Mail. Behind the scenes Mail stores your messages in a file called an “mbox”. This is an open source format that many applications use such as Mozilla’s Thunderbird. In fact you can import messages into Microsoft’s Entourage by dragging an mbox file onto “My Messages”.
Storing your messages in mboxes also makes them easier to back up. You can find your mboxes in the Mail folder that is inside your own Library folder – you will see a folder called “IMAP-your-email-address” if you use an IMAP account and/or you will see a folder called “POP-your-email-address” if you use POP3.
Inside these folders you will see an mbox file for each “folder” you have in Mail. You will see an “Inbox.imapmbox”, “Deleted Messages.imapmbox”, “Sent Messages.imapmbox” and so on. If you want to keep messages from “Client A” in your Mail application and you make a rule to move the messages you have received into a folder, Mail will make a file called “Client A.mbox”.
To make a new Mailbox in Mail:
Choose “New Mailbox” from the Mail menu.
Select “On my Mac” as the location.
Name it “Client A”. (or whatever name you like)
Press OK.

Then select a message from Client A.
Go to Preferences under the Mail menu.
Choose Rules.
Choose Add Rule (or edit)
set it to:
If [Any] of the following conditions are met.
[From] [Contains] “@clientadomain…”
Perform the following actions:
[Move Message] to mailbox: [Client A]
Press OK.

Then when you “Apply Rules” it will move the messages to the “Client A” mailbox/mbox and any new email you receive will go to that folder automatically.

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