Pop accounts and .Mac with Mail system

Iv been trying to learn how to use my iBooks 'mail' system with both my Gmail and .Mac accounts. But, keep coming up with more questions than I can find answers to.
1. Why doesn't mail that I receive or send from my 'mail' programme show up when I go to .Mac and open the mail there? Shouldn't the mail be in both?
2. Same question for folders that I created in both .Mac and the 'mail' system.
3. When using the 'mail' system with POP accounts does deleting mail automatically also delete the mail in the original POP account. In other words if I have the 'mail' system set to delete POP mail for a Gmail account does that also delete the copy over in Gmail?
Just trying to figure out how the 'mail' system works in relation to if I use .Mac. Also, in relation to Gmail. I'm learning that when I'm in .Mac things aren't quite the same.
Thank for the help in advance.

You can access multiple accounts with the Mail.app and each account has its own webmail access that does not reflect all mailboxes available with an email client such as the Mail.app. It is impossible for webmail access with your .Mac account to reflect your Gmail, Yahoo or any other non-.Mac account mailboxes or any user created "On My Mac" location mailboxes which are stored locally on the hard drive.
The same when accessing your Gmail or Yahoo account via webmail access using a browser. Doing so will reflect your Gmail or Yahoo account mailboxes only.
When logged in to your .Mac account via webmail access using a browser, it will reflect your .Mac account's inbox mailbox in Mail and any other .Mac server stored mailboxes in Mail which are located under your .Mac account named icon in the mailboxes drawer only. It will not reflect the mailboxes for any other account, any imported mailboxes or user created "On My Mac" location mailboxes.
> Sounds like what you're saying that in order for both .Mac and my mail.app to sync they both have to be marked ".Mac account" and not "on my Mac". That way they both operate from the main Mac server. Am I heading in the right direction?
Not exactly.
The Mail.app mailboxes drawer includes the following in this order:
* Inbox
* Drafts
* Sent
* Trash
* Junk (only if Junk Mail is set to automatic)
* Smart Mailboxes (only if you have created and are using any Smart Mailboxes)
* Imported Mailboxes (only if you have imported any mailboxes)
* User Created "On My Mac" location mailboxes.
* .Mac account named icon
The Inbox mailbox for each account is located under Inbox in the mailboxes drawer regardless the account type. Open Inbox in the mailboxes drawer by selecting the black triangle beside it pointing it down to reveal the account named Inbox mailbox for each account. Selecting an account named Inbox mailbox in the mailboxes drawer reveals messages received by that account only in the message list. Selecting Inbox in the mailboxes drawer reveals a blended Inbox mailbox for all accounts.
Your .Mac account's Inbox mailbox in the mailboxes drawer is synchronized with the server which is the same behavior with any IMAP account. Messages in your Gmail or Yahoo account's Inbox mailbox are downloaded from the server, not synchronized with the Gmail or Yahoo servers and the same with any POP account. It is impossible for your .Mac account to synchronize the Inbox mailbox for a non-.Mac account.
Go to Mail > Preferences > Accounts and under the Mailbox Behaviors tab for your .Mac account preferences, if you don't store Drafts, Sent, Trash and Junk messages on the server with your .Mac account when using Mail, the account's Drafts, Sent, Trash and Junk mailboxes will be available under the Drafts, Sent, Trash and Junk categories in the mailboxes drawer. All account mailboxes under Drafts, Sent, Trash and Junk in the mailboxes drawer are stored locally on the hard drive.
Open your .Mac account named icon in the mailboxes drawer. All mailboxes under your .Mac account named icon represent/refelect your .Mac account server stored mailboxes when accessing the account via webmail EXCEPT for the account's Inbox mailbox which is located under Inbox in the mailboxes drawer. If you don't select store Drafts, Sent, Trash and Junk messages on the server under the Mailbox Behaviors tab for the account preferences, besides your .Mac account's Inbox mailbox, no other mailboxes are and can be synchronized with the server except for the mailboxes located under your .Mac account named icon in the mailboxes drawer.
When creating a new mailbox, you can select "On My Mac" as the location which is stored locally on the hard drive and will not be synchronized with the server or any server.
Or you can select your .Mac account as the location which will create a server stored mailbox which will be located under your .Mac account named icon in the mailboxes drawer and will be available on the server (via webmail access) and kept synchronized with the server.
No other mailboxes in Mail will be available on the server with your .Mac account via webmail access and this is the same behavior with any email client such as the Mail.app.
> Is this something I should ring up Applecare on to make it simpler to make them match? Or would changing them all to ".Mac account" and the server solve the issue?
Calling AppleCare will be a waste of time because your problem is a lack of knowledge and understanding only. You can't change your Gmail or Yahoo email accounts to a .Mac account with Mail or with any email client since these are separate/different accounts.

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