Ho John, since SF isn't answering, I'll answer for you.
The SF WordPress system will NOT allow you to use your own or custom themes. There is however quite a few different styles to choose from. They also limit the plugins you can access due to theme compatibility and security issues. So, you have to do manual installs for most plugins and can't use some altogether due to conflicts & permission restrictions.
As far as your domain is concerned, you will just have to update the Nameservers to point to the ShareFaith servers. It's pretty quick and easy.