When you first start Retroarch, it should ask you "Hey, what consoles do you want?". You go through and select the ones you want, and then it'll silently poll your machine's specs, and download the appropriate recommended cores. Then, it should ask you to map out your controller based on the common Xinput standard, and ask if you want any two-button controllers (NES, PCE, SMS, etc) to map their left and right buttons to X & A, or A & B respectively. Then, ask you to point each console to its appropriate rom directory, and just let you access your roms as-is from there.