I believe some of the videos on remapping core input in the Retropie Wiki about Retroarch should work the same for the windows version (I haven't done it yet, but probably will here in the near future): https://github.com/retropie/retropie-setup/wiki/retroarch-configuration
I forget how many nice little things are in retropie like the ES auto-configs for Retroarch that don't always work when you do things separately (and/or on Windows). When I did try Retroarch on Android the core input mapping did work the same as it does in Retropie as shown in the wiki video links.