By adding the following lines to my retroarch_core_options.cfg (/opt/retropie/configs/all) I was able to bypass the Dual Shock warning:
pcsx_rearmed_pad1type = “analog”
pcsx_rearmed_pad2type = “analog”
Mind you the game I’m using this as a test for is Ape Escape. It seemed to work, with the exception of being up to get the character to react by moving the right stick forward. Also, when I now try any other games, none of the control works.