The portfolio URLs in Flexform by standard follow the following format:
?portfolio=item-name
If this isn’t to your liking, then it can easily be changed to use this format:
/portfolio/item-name
All you have to do is edit /includes/custom-post-types/portfolio-type.php, change line 48 to:
'rewrite' => true
and line 50 to:
'has_archive' => false,
Then, as long as you have permalinks enabled (not default) in Settings > Permalinks, you will have SEO friendly URLs.
If you’d like not to have /portfolio in the URL, then try this plugin:
http://wordpress.org/extend/plugins/remove-slug-from-custom-post-type/
– Ed