Best USB arduino version for etched PCB?

Hi there,

I would really like to make cut my own arduino board. I have access to one of those old school PCB etching machine at university.

Please could you guys give me some advice? If I want a bob standard arduino board, with USB and atmega328, and I want the board to have as many through hole components as possible, what version of board and associated EAGLE files should I be hunting for? I would like the board to be completely shield compatible. The PCB machine can do double sided boards. A version with as few via point as possible is preferred.

Also, what's the easiest way to burn the bootloader onto the uC?

Thank you all in advance for your help, it is greatly appreciated!