How to drush up multisite? I am not clear after reading another question on same topic how this is done.

At the moment I go to my root drupal install and drushup then updatedb so if I then go 
to the folder of a multisite and try to drushup it says nothing to update.

If all the modules are in the root drupal install is that sufficient? Could you not make sure they are all placed in there so you would need to only drushup the root folder?

How then do you update individual databases?
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.