So this sounds like something that happened to my friend. He had 2 of the same gamepad the problem was that when we went to input and changed the input to another device, the name didn't change therefore we weren't sure that it was even reading both seperately. We fixed it by taking what we considered p1, moving the device name in the emulators input config to the far left, and configured our buttons. Now when we went to set up player 2 we started far left then clicked one to the right. The name didn't change but it did in fact pick the other controller. We then set up accordingly.
I don't really get what you mean. L3 and R3 are buttons, not triggers. Only L2 and R2 can eventually be triggers, depending on the pads. Easy to notice : when you map triggers in ES, they are marked as Axis, not buttons. The analog joysticks are handled, no problem with that.
I'm sure i didn't answer your question :o but recalbox handles everything itself : hats, buttons and triggers/axis, and sets the emulatir up accordingly.