There is one main connector (it's a 60pin if I remember right), that plugs directly into the PCM. This may or may not have to be removed. I had to remove mine to get the PCM out. No biggie, just one bolt that holds it in. There are 3 other plugs/harnesses that run directly in front of the PCM (you'll see them when you take the kick panel off), the middle one will need to be unplugged, the two outer ones can be moved out of the way, and the PCM should slide out between them. Once the chip is installed, the PCM will probably NOT fit back in where that plastic bracket is. Simply break the bracket off (much easier than unbolting it) and it should fit back in.
EDIT: I forgot the most important part. ANYTIME you are working with the PCM, unhook the battery and turn on your headlight switch, and let the car sit for AT LEAST 10-15 minutes!! This will drain any residual power in the electrical system, preventing your PCM from getting fried when unplugging/plugging in the connections.
Oh yea, make sure to clean that J3 port EXTREMELY WELL!! Rubbing alcohol and a pencil eraser works really well.