half the answer
To set up your iPhone mail to work with one of your aliases, just set up a new account. iPhone Setting-->Mail, Contacts, Calendars-->Add Account-->Other. Then fill out the information, using your alias as the email address, but your main AppleID for User Name.
That gets you your alias inbox, and the option to select that email address in the "From" field.
The reason this is "half the answer" is because, for the last couple days, my alias inbox has not been able to load any of my email content. New messages appear, but if I touch on them, the "Loading..." message spins forever, and no content loads.
Apple's phone support hadn't heard of the problem. I've restored, reset, etc, but with no luck. I'm going to the store Thursday to see what the geniuses can do. Hmmm, maybe I'll get a free 3G and the beta version of 3.0 with support for all of Apple's features. That would be neat.
I'll post back here with any new info