[apple007]

The only solution I can think of to the two-devices-checking-same-POP-email-account issue is to go into Mail's preferences, click on the account(s), click on the Advanced tab, and then change the setting from "delete message immediately" to "leave message on server" for anywhere from 1 day to 1 week. This should result in all new emails showing up on both devices, even if both are on and checking your account(s) at the same time.

As for your general sync issue, I thought all emails were synced from the main Mail.app to the Mail app on iPhone every time the two devices are connected/synced. I don't have an iPhone yet, but I thought that was supposed to be the deal (??). I'm sure someone else can chime in on that.