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