Hello,
The logo is located here where you can edit it:
templates/s5_digital_systems/images/s5_logo.jpg
As for setting up the menu check out the homepage here, we explain what to do for setting up the menus:
http://shape5.com/demo/digital_systems/If you'd like to test before you buy I recommend checking out the "Vertex" or "Design Control" templates as they are a lot more advanced that "Digital Systems"
Cheers!