sub domains or sub directories

Hi all.
I have just installed a new WPMU site on a new account (with dedicated IP) on my server. I chose sub domains as the method for creating new WP sites. However it seems that I can not just press "new site" in the WPMU dashboard and create a new site as I need to go into cpanel to create the subdomain (this may sound obvious to you so I apologise).

I would rather have a simpler way to create sites, so Im thinking, would using sub-directories as a way to create new sites be a lot simpler? I then want to use the domain mapping plugin to give each site the option of having its own domain mapped to it.

Can I make some changes now before I have created any posts / pages etc or do I have to make a new install from scratch?