I think I figured it out myself… I’m not sure if this is the correct way, but it is the only way I could get it to connect and reconnect after turning off the controller. Also, if a PS3 controller was already paired this method did not work (not sure why)… this only works on a fresh RP image and was tested on v3.0 B4:
# SSH or go the command line:
# Install/Launch PiAssist
$ wget https://raw.githubusercontent.com/Death259/PiAssist/master/PiAssist.sh
$ chmod +x PiAssist.sh
$ sudo ./PiAssist.sh
# Pair Controller via Bluetooth menu, very simple
# Edit rc.local
$ sudo nano /etc/rc.local
# Paste the following after “this file does nothing…”
#!/bin/bash
hciconfig device up
hciconfig set name raspberrypi-0
hciconfig set class 0x420100
hciconfig enable iscan
hciconfig enable pscan
# Change class to value from /var/lib/bluetooth/xxx/config
# This whole bit allows reconnection later without having to re-pair
# Save/Exit
CTRL + X, Y, Return
# Reboot
$ sudo reboot