How to drush up multisite?
There is Aegir, which is a system that helps you with doing that.

I personally have no experience with it, but I attended a talk on it a few weeks ago and it totally does the job.

In general, it gives you an admin interface of all your sites on that drupal installation while letting you update each one individually. It automatically rolls back if something fails.

Go have a look: http://www.aegirproject.org/

It probably is overkill with just two or three sites, but it seems to help a lot with bigger sites.