I have the USB Autoprom from Moates.net. The ECM was modded with the G2 adapter from moates.net, to allow me to use a 27SF512 EEPROM. This takes car of the chip burning, and emulation. You would hook the cable up to the socket in the ECM, and upload a bin to the autoprom. The car will run on the autoprom, and accept real time changes to the bin file. you could also use winALDL to datalog through the ALDL port, but I just use tunerpro RT to datalog. When I am happy with the bin, shut down the car, burn a chip, and drop it in.
Now, TurboTweak has the poop with being able to change your spark and fuel with no other tools, but if you are anal with you idle and all like me, I like to tune my own stuff if I can.