When you are on the index page the logo at the top is just an img tag inside of a link, here is the html for the image:
<img width="154" height="79" alt="Power CMS" src="../images/logo.png"/>
If you replaced this image with your own and adjusted this tag on the index page you can use your own image.
If you would like to make use of your own css just add it in the list of the loaded css files, so long as it appears last in this list it will take precedence over the default css files.