The easiest way I've discovered is to simply replace logo.gif (or logo.jpg - sorry I can't remember the proper format off the top of my head) that exists in your directory with your own logo. Just use the same file name and dimensions. If you have to use different image dimensions than the PowerCMS logo file, you'll have to edit the image attributes in the php page(s) manually to match your own. Other page characteristics such as background color, text and link colors can be changed to match your branding by editing the CSS.
I've done this with PowerCMSBuilder in which the logo.gif is placed inside the images folder after install. Not sure if its located in a different spot if you're using the older stand alone version of PowerCMS.