I'm on the same predicament. Configuring a controller is really confusing and anything but simple nor friendly.
I'm trying to configure my 8BitDo SN30pro USB gamepad to use it on BlastEm, but all I could find is a general configuration file on my Windows user folder with a lot of bindings already set, how am I supposed to use my gamepad (in a simple way).
Looks like devs found the most confusing way to do it.
By now I'll still keep using Kega, as simple as it can be and user friendly at its most.