Arduino ATmega32u4 low-power bootloader

We have a board with a ATmega32U4 MCU that comes preprogrammed with ATMEL bootloader and we need it to be Arduino compatible but in a low power mode (board current consumption <1mA @3V). We need someone with Arduino/AVR skills to be able to write a simple tutorial and send us the correct files/bootloader to burn into this board. PS-The board has the 3x2 pins ISP pads (MOSI, MISO, CLK, RESET, VCC, GND) to connect a programmer. I have an AVR mkII programmer and I intend to use it only one time to lower the consumption. Then we want to use a micro USB connector to change the Arduino sketches. Hardware we have: ATmega32U4 and it's 0.1uF capacitors and a 16MHz crystal (+ 2x 22pF caps). Tips: We've been searching and we know we have to change the fuses to prevent the brown-out-reset (BOR) when the battery is lower than a certain voltage. We'd also have to change the CLK bits to divide the 16MHz crystal into a lower frequency mode to consume less energy. We found this webpage that explains how to change the fuses: [login to view URL] We just don't know how to do this in Arduino or Avrdude and if by doing this bootloader change the board would still be recognized in the Arduino 1.0 program (boards sections - like a Leonardo variant 8MHz for example).