If I understand your question correctly, iCal allows you to pick any email address that you have setup in Mail.
Make an event in iCal, next to 'alarm' choose 'email'.
In your case it will autofill with your MSN address, but if you click that address iCal should display the other email accounts that Mail knows about.
It has nothing to do with what e-mail you have set up in Mail.Just tried it. Won't do it. Only email address it shows is the MSN account.
The MSN account is my Apple ID for iTunes and the like. Is it something to do with that?
It has nothing to do with what e-mail you have set up in Mail.
Try adding the e-mail address you want to use to your contact info in Address Book.