Wow, I actually made some progress - I found a libretro guide that points out that the kickstart roms need to be renamed, and now running P-UAE gives me the Kickstart 1.3 A500 screen...
But I don't know how to make it load my A1200 rom instead, nor make it load an ADF file (the uae config file seems to get automatically generated and my edits removed!?)
Do people use another add-on or something, to browse and configure the launching of P-UAE for specific game titles..?