Hello!
New user here. I did a fresh install after completing a setup of 3.0 RetroPie a month or so ago. I wanted to start over from the beginning and try to clean up some things from my first go around. One thing I noticed with 3.2.1 is the PS3 pairing was a breeze. I merely plugged in my JBTek Bluetooth dongle and booted up the image for the first time. I ran the PS3 controller driver installation from the Setup. After the driver was installed, and it gave the text to unplug the USB and pair, I did exactly that. I unplugged the controller and pushed the PS button. It paired almost immediately.
Is it giving you an error? Do you see the message that tells you to unplug and pair the controller? It should be as simple as pushing the PS button and let it do its magic. I also had to modify the Bluetooth setting with 3.0 to keep scanning to allow two controllers to pair. This was not the case for 3.2.1. I paired both controllers after the first installation.
Sorry if I misunderstood and this doesn’t answer your question. If not give a bit more detail of the point at which you are stuck. Have a pleasant day!