amiberry controller config when launching from emulationstation

[electricaltill]

RetroPie 4.4
Raspberry Pi 3B
Itrunk 2.5A PSU
Built from retropie.org.uk
Controller: 2x 360 pad

Hi all, noob here (linux and amiberry). I'm sorry if this has been asked elsewhere; I've tried searching but I'm not sure what terms to use.

I have a pi 3, official PSU. I'm trying to run games on amiberry and struggling with the controller config. I'd like to run it with 2 360 pads, but without having to have a mouse/keyboard attached. So I need one of the joypads to be able to send mouse presses to get past the cracktro on many games. I find it weird that with 2 joypads attached the emulator doesn't process the fire button on the second joypad the same as a mouse click (which the Amiga did), but that's neither here nor there.

If I launch games from amiberry rather than from emulationstation I can configure the bumpers on one pad to send left/right mouse presses and save that as a configuration. The problem is that I can't navigate the amiberry menus using a joypad - a single button press tends to register as two or three presses in amiberry, so it's impossible to do certain things. So unless I can fix this behaviour I need to run games from emulationstation.

When I do that, my 'mouse joypad' configuration isn't used, even if I saved it in amiberry as the default configuration. What configuration is used if I open games from emulationstation, and how do I change it?