Sync With Apple Mail

Hi All
I have just bought an iPhone and I am really confused about the Mail side of things and was hoping someone could put me straight.
I use Apple's mail client into POP3 accounts and .Mac mail.
Before I had the iPhone I had my POP3 email set in in Apple Mail to pull down any new messages every minute and leave any messages on the server for a week in case I wanted to see them when using a web client.
I set up iPhone and it downloaded all the messages off the server/s. So, now I have two different inboxes - my 'main' one - Apple Mail - and the iPhone which are different at all times no matter whether I delete messages in Apple Mail or not.
So, I thought it might be better to set Apple Mail to pull messages off the servers completely when it checks each minute and delete any sent mail off the servers too. I would use the iPhone to show me stuff that comes in while I am away from my Mac. (I would have to quit Apple Mail for this to work if I left my Mac on).
Is this the way that you are meant to set the thing up? I had hoped that the iPhone would just look like my Apple Mail inbox but doesn't seem possible if iPhone references what is on the server directly.
So, I get even more confused when I press the curved arrow button at the bottom of an account's inbox and nothing changes to the list of emails on the iPhone. They should all disappear I would have thought now (given that all the emails have gone from the servers courtesy of Apple Mail's 'new' settings).
I hope someone can decipher my babble and help me out!
All the best
David

Yes - with POP3 the iPhone and Apple Mail downloads a copy of whatever is on the server. What then happens to those messages on the server is determined by your mail settings - whether the messages on the server are deleted immediately, at a later date, or never.
Yes - emails deleted on the iPhone/Apple Mail has no effect on what happens on the server with POP3 accounts. With an IMAP account, however, emails would be deleted off the server.
Emails sent from the iPhone do not register as sent with the POP3 server and therefore will not get picked up by Apple Mail (and vice versa). You effectively have two outboxes. An IMAP account, however, would allow you to sync the two.
You should be able to change your POP3 email to IMAP, although you may have to pay for it if you're using a freebie email address.

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