What about .Mac users? That's IMAP isn't it? All I know is that when I check my e-mail at another computer, via .Mac's webpage, anything I do (delete, move, etc.) is reflected in my Mail.app when I get home (and vice versa). I never have to manually "match" the two.
I'm hoping iPhone does the same thing? If I get an e-mail and delete it on iPhone, it's deleted on my PowerBook when I get home? I've never had to screw around with my .Mac mail, in terms of keeping the web-based mail match my Mail.app.