Somehow I enabled the controller configuration window by clicking a couple of buttons on the external gamepad.

Did you updated your controllers with the last firmware and used the start mode of the https://github.com/recalbox/recalbox-os/wiki/8bitdo-on-recalbox-(EN) ?

Hello sorry for my english. To configure controller for mupen64plus you add controller into /usr/share/mupen64plus/InputAutoCfg.ini Use use this command line to know the position of buttons and joysticks

There is an example into this post : http://blog.recalbox.com/forums/topic/configuration-manette-mupen64plus/ (French)