2. That is a normal occurrence: https://www.petrockblock.com/forums/topic/how-does-a-controller-get-auto-assigned-a-config-profile/ unless of course it said it configured .cfg and never gave you a chance to configure it then that is not normal- make sure you only have one controller plugged in before you attempt retroarch configurations.
3: when opening a game press x or m on a keyboard and it will open up into a menu where you can choose which emulator you want for each ROM or system. You can also modify video settings from this menu. The retropie wiki indicates where to place ROMs for each respective emulator: https://github.com/retropie/RetroPie-Setup/wiki
BTW the more information you can give about your setup the more people can help you with your problems :)