JTAG, arduino Duemilanove, ATmega  88P question

I have an arduino Duemilanove. I have used the original microchip (ATmega 328) on a certain device and I have several ATmega 88P available. I also have an atmel JTAGICE mkII.

I would like to burn the program I wrote with the arduino onto the ATmega 88P microchips.

The way I look at it I have two options:

  1. Use AVR studio and the JTAGICE mkII to flash the memory onto the microchip using the ICSP 6-pin headers.
  2. Use the arduino environment with the JTAGICE mkII to load a bootloader, and then upload the program using the USB connection on the arduino.

Can someone please provide me with detailed instructions on how to achieve either one of the two options listed above.

Thanks for the help,