I don't want to sound insensitive, and it's uncharacteristic of me to scare you, but you will NEED to learn this stuff fast. You have purchased a modified car and it will not behave like a stock Honda Civic that you drive off the lot with a warranty. There is major potential for this car to have seriously compromised longevity if it is not properly cared for. I would begin by reading these links (all of them): Unabomber's Manifesto - NASIOC.
If you have any questions, post them up here; we will help you. In the meantime, call Cobb and ask for their assistance (Cobb has fantastic customer service) regarding map flashing and reading your CEL.