We currently intend for the new illustrations to be for the existing sample characters (both from Bulletproof Blues 1e and the two Character Art Packs currently on DriveThruRPG). That might change, but that's currently the plan.
However, there are two ways (at the moment) for people to get their own characters in the published game. The easiest is to submit a character to the GagMen Podcast contest. I can't urge people enough to take part in that: it's a great contest and so far, there's not a huge amount of competition, so your chances are really quite good!
(See https://www.kickstarter.com/projects/948204445/bulletproof-blues-second-edition/posts/754633 for more info)
Also, anyone who backs the Kickstarter at the KALOS TEAM-UP level ($250) gets a high-resolution illustration of their character by Sean Izaakse, and the character will be featured in Bulletproof Blues Second Edition.
Finally, anyone can submit their character to us to be added to the Kalos Universe web site ( http://wiki.kaloscomics.com/ ). We don't provide the artwork for it, but if you do, we'll add that to the Kalos Universe site as well. Our goal is to have the Kalos Universe site grow and become a huge, free resource for players and GMs.