New Wordpress MU Site Being built

Hi, thanks for taking a moment.
I'm setting up/building a new mu site.
I usually set my permalinks to
/%category%/%postname%/
Will this be ok for an mu install/set up?
Is there a better configuration that you would recommend?
I will have a main site at "mydomain.com"
I will have additional themes installed on
"mydomain.com/themeA"
I will install the pro -sites plugin to allow users to create/have their own blog on the site.
What set up would you recommend?
Do I just set it once for the main site url/settings?
Thanks for your help & patience,
Jon