1) Get an ISP e.g. AVRISP MKII.
2) Build the relevant circuit to interact with the above kit.
3) Upload your bootloader to the chip.
4) Use the chip as per described in the Nerdkit manual e.g. build the basic circuit to upload the user progs and power ahead!
Your steps are real close, the only additional steps would be to modify the makefile for the type of programmer you are using, and upload new fuse/lock bit settings to the chip. Those would go between your steps 2 & 3.
As for a relevant circuit, you can use the NK base setup only replace the jumper wire that connects pin1 to the 5v rail with a 10k resistor. This will allow the programmer (which has a wire that goes to pin1 (reset)) to toggle the reset line. The other connections to the microcontroller will be on pins 17 (MOSI), 18 (MISO), 19 (SCK), and VCC (5V) and GND.
I've just looked at the AVRISP manual and I can see how that lines up.
FYI to anyone reading this post, the manual is here, page 26 for ISP pin outs.