Whoops Deja Vu,I forgot to break this down.
Did you read the help screen on startup?
X confirms
Z cancels
Enter defaults a highlighted option
F toggles fullscreen
F1 toggles the GUI when ingame
In the settings>input options go to Input user 1 binds>user 1 bind all then you will input your controller buttons 1 at a time.
Set it up just like a SNES and PSX pad Exactly as this is how every emulator control is set up until you load a game then you can change button keys.
Retroarch is meant for almost full controller use since the authors made it for a consolized emulation experience, it controls mostly everything.
You should use a Nightly build, the one you want is titled Retroarch.7z, it should be on the bottom of the windows nightly 64 bit.
I really need to make my tutorial................
RA is not hard at all to use, it makes using the stand emulators easy as pie to setup and run since once you set up the standard options then everything is setup and ready to use unless you need a slight tweak in the emulators core/input options.
Any other questions ask away and il answer them to the best of my ability.