If you domain map, then the format you pick is irrelevant.
For ones that you leave as-is, the SEO are slightly different and depend on what you want to accomplish. Subfolders are seen as part of the main site and will strengthen the domain authority of the main domain. Subdomains will give separate results in search engines.
These forums were CLOSED to new posts on November 19th, 2012. New forums are here: http://www.studiopress.com/forums/
and you will need to SIGN UP AGAIN.
If you need assitance with setting up your theme, go to http://my.studiopress.com/
and read the SETUP links or the TUTORIALS link on the side tab.
If you need Account Assistance
, file a help desk ticket at the same location.