I'm taking the CA PE in Spring 2016. You submit LiveScan with your application. There's a form on the website that has 3 copies. You take them to LiveScan. They keep one, give you one and you include one with the application.
I have colleagues who are taking the exam in October and submitted their application prior to July when this took effect but they still have to submit LiveScan so they get their license once they pass the exam.
If I were you, I'd send it in with the application. That's what I'm doing. The LiveScan form says: "Second Copy – Return this page with your application along with the applicable application and examination fees to the Board to the address at the top of the application. Without that form, we will be unable to retrieve your results from DOJ and FBI."
http://www.bpelsg.ca.gov/pubs/forms/gg_live_scan_5_15.pdf