Custom taxonomy and post type rewrite rules

I hope i understand you 🙂

I think the easiet way (in my humble opion) the best way is to use taxomonies like so:

function portfolio_taxomony() {
register_taxonomy( 'portfolio', 'post', array( 'hierarchical' => true, 'label' => 'Web Design', 'query_var' => true, 'rewrite' => true ) );  
}

add_action( 'init', 'portfolio_taxomony', 0 );  

(Web Design if of course an example)

That way you’ll have a url like this:
http://www.site.com/portfolio/web-design/postname/

To me that looks great from an seo point of view because the url is like a “story” and also, easy to do..