@lesk You would pair it just like for a PC (Windows). Normally just press Start for 3 seconds and it will start to blink blue with one pulse. I'd suggest you reset the controller to the defaults, remove the BT pairing from RetroPie and start again using the PC mode and do the pairing and then reconfiguring in ES.
I did this. But still it does not work in any game. Only in Emulationstation as I stated before.
I tried one thing last night. While connected via bluetooth I went into config and then retroarch.
There I found user binding(or something like that under inputs) and I used my controller and rebind all the keys there, and pressed auto save config.
Aaaaaand I could use it in game! But the hotkeys dont work. I cant quit games, cant load save slots or change save slots. So im still puzzled.