ok I'm an idiot....I didn't realize when I first mapped my ps3 control to retropie - that the ps3 controller numbers are right there as well..dpad up is 13, dpad 14, then I just needed to go to the dapinput.ini and add 1 to all the numbers since 0 is an unmapped number
There was a fix to Daphne by @werpu one and a half year ago (see here). It added a command line option -joynum followed by the controllers system index number, e.g. 0 or 1 to set the controller being used.
It isn't clear to me, though, if the number is the joystick index (jsX) or the event index (eventX). So, here the commands to show both of them:
evtest # lists all devices connected to an event
jstest /dev/input/js0 # change 0 to 1, 2, 3 etc. to see the device using it. Exit with Ctrl-c.
input configuration script doesn't refer to the joypad anyway but i find that unlikely.
I haven't tested it myself, but I assume the new input configuration script is referring to the mapping of buttons only. Daphne is an emulator that grabs the first joystick event it can find and there is no way to configure it to do otherwise outside of an external mapping solution.
A tip to hopefully make your joystick appear as the first event is to plug into the upper left USB port. If that doesn't work, then try launching Daphne while it is the only USB device plugged in at all. If that also fails, you're left with very few options other than key-mapping your controller to fool the system into thinking it's a keyboard.