Assuming you are using the latest version of Retropie, you did not mention your build other than a wired 360 controller. You should read this: https://retropie.org.uk/forum/topic/3/read-this-first Then the following:
If you had your controller plugged in when you booted up it should have asked you about controller configuration. If so, this tells you everything you need to know about configuring a controller. Follow these and you'll be gaming in no time.
https://github.com/RetroPie/RetroPie-Setup/wiki/RetroArch-Configuration
https://github.com/RetroPie/RetroPie-Setup/wiki/Controller-Configuration