What the OP is asking is to only receive a single notification (aka alert) when a PM is waiting and not receive any additional alerts on subsequent PMs until he has logged in and read his PM's at which point the alert sent indicator would be reset. This is the way many commercial alert notification systems work. It's also a users personal choice preference as I think most would like to individual alerts for each PM.
Client side configuration is okay, but a real email server/service with IMAP is the way to go. Mail processing takes place on the server side and is then available to all mail clients.