Just got off the phone with them... Here's the breakdown:
You order it from their website for $490.
They call you and you tell them your exact configuration (intake, headers, catback, pulleys, etc), and they tune your ECU based on what you already have on your car.. Very cool.
ALSO, if you ever add a modification to your car in the future (headers eventually for me probably), they just charge a $100 reflash fee to optimize your ECU for your new modification.
They said that the 09s have a different ECU than the 08s, and it makes it a little more complicated to modify them, but that won't be an issue for me since mine's an 08.
Also, they said, despite the outdated .pdf about the Hyundai Accent on their website, they've done extensive testing of 07s 08s and 09s lately, including road tests, and they've gotten some pretty impressive gains of HP and torque.
In summary, I'm totally getting mine reflashed within a month.