hmm I have zero delay encoders I don't remember if I had to set them up in RetroArch or MAME or if they were just seen like a regular xinput controller I'm leaning towards not having to config them in the emulators.
For LaunchBox and BigBox there are separate config for controllers for LB you go to Tools Options and you enable your controllers if you want to use multiple controllers with LB check the use multiple controller checkbox if you have any issues with the joystick being uncontrollable try turning off z axis scrolling.
For BB when it opens to the platform view press the back button and go in to options controllers and you can enable and set your options there