Help managing mail  between computer/phone

My problem is that even as I delete messages off my Mac email client, they remain on my iphone mail. This remains after docking. Therefore, while I only have 10-15 messages in my mailbox, I have 176 in my iPhone mail.
Some things I have tried:
Repeated fetching on iPhone.
Repeated docking / syncing.
Any help would be appreciated. I would like to know:
1) If deleting off of Computer Mail can be set to remove messages from iPhone mail
2) If deleting off of iPhone mail can be set to remove messages from Computer Mail
3) Any other information relating to this issue.
Details follow:
Under the advanced settings, under deleted messages remove is set to "Never", and under incoming settings, "delete from server" is also set to "Never" These are the only two that I could possibly connect, however I have been unable to locate information about what they may actually mean so have resisted playing with them.
I am working off a brand new iPhone 3Gs.
Computer system is MacBookPro, running OS X 10.5.8, but I have no updated to Snow Leopard. Other stats 2.2GHz, 2GB @ 667 Mhz.
I am using my school's email (and @edu address) and I have it set up to my Mac mail client as a POP account. I can also set it as IMAP, but as I understand POP transfers messages to local storage and DOES NOT leave a copy on server, this is my desired setting.
Mail is version 3.6(936). Its the standard mac client (ya know, the eagle stamp)

You're welcome.
The server is the "master" for an IMAP account.
With an IMAP account, all server stored mailboxes are kept synchronized with the server with each email client used to access the account.
You have the option to store the account's Trash mailbox on the server or locally with each email client used to access the account. If you store the account's Trash mailbox on the server with each email client used to access the account, selecting a message for deletion with the Mail.app on your Mac will move the message to the account's server stored Trash mailbox making the message available in the account's Trash mailbox with the iPhone's Mail client on vice-versa.
After sending a message with the iPhone's Mail client, the sent message will be available in the account's Sent mailbox automatically with the Mail.app on your Mac, and vice versa.
All server stored mailboxes with an IMAP account will be identical with each email client used to access the account since all server stored mailboxes with an IMAP account are kept synchronized with the server automatically with each email client used to access the account without having to do anything special.

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