I would recommend something based off the Duemilanove if it meets your requirements. The ATMega328P is a lot easier to work with I find and I have built a few PCBs with them myself so I am a little more familiar with them.
The top right corner of that schematic is completely useless, it is additional documentation on what outputs are associated with which pins, just in a clearer way than is demonstrated on the top left. The main things you need are the USB connections, Crystal with load capacitors, pull up resistor on the reset line & the ICSP header. A lot of the other ‘stuff’ is optional. Although I would keep the 22 ohm resistors inline with the D+ and D- usb signals.
In an ideal world the USB traces should be impedance matched as they can be high speed signals. Doing this in eagle (which i assume you are using) is a bit of a pain and not really required for a micro like this one, provided you keep the traces short.
If you have more specific questions I can be a bit more useful.