integrating due, ethernet shield with my project on a pcb

I am using due with my project and I need to make a pcb including my circuit and the arduino due circuit on the same pcb. Some of the features that i need are ethernet, sdcard, usb, spi and a bunch of other lines.

What is the best way to go about it. Should I start with the datasheets of the chips and start from scratch or take the due and ethernet shield schematics, merge them somehow and then remove the unnecessary parts. What are some of the obvious candidates for removal. Any dos or donts for this approach? This is my first time doing this kind of a thing, so any help is appreciated.

Initially build Basic circuit with due like uploading program . Check basic functionality work or not like blinking led.There software Circuit labs . Where you can do simulation.

Thanx, I will check out the circuit labs software. I have to wait for the processor to arrive before i can try things out.

In the meantime, I started removing the unnecessary stuff from the due schematic. I got rid of most of that, but I am a little confused about the uOTGVBOF circuit (below the bottom right of the chip), using the opamps and p channel mosfets. There is a comment below the circuit that goes like this -

Forces OFF the power supply to USB port when the USB port is in HOST mode
(board powered from external power supply)

Whats the impact if I remove this circuit. I dont plan to use the usb in host mode, it will only be used for uploading the sketches or connecting to pc for debugging purposes. Is there going to be an issue if someone unintentionally connects some other device to this, say a kbd or mouse etc, if the board is powered from the external power supply.

Also, this part of the circuit is controlling two lines USBVCC and USBVCCU2. USBVCC has control logic, but USBVCCU2 doesnt have any. Whats the difference in these two lines.

Edit: Schematic image is attached.