AAh yes the glorious world of zynthian encoder config…
I have to relearn it everytime I REALLY muck around!
A bit of history helps.
The Zynthian started out on the standard GPIO pins and, indeed you can build the original 4 encoder zynth with nothing more than a gpio connector and … 4 encoders.
But which pin on which encoder goes to which pin on the GPIO pins…? Do they all work …? how do I work out what goes where.
Well A Build with Variations variation: HiFiBerry Amp+ goes some of the way to describe the process, and
Encoder mapping for Direct I/O connection - #9 by wyleu shows the mapping in a nice chart . . . .
!!! THE ZYNTHIAN WEBCONF NUMBERING IS WPi !!!
The Wpi pins match the numbers that go in the Zynthian webconf, so you can use this chart to allocate appropriately. The SPI errors listed are something hat just seems to have magically occured so avoid those pins and ignore the rgb encoders that was a fanciful bit of playing around, that never made it to zynthian code.
Basically you specify the GPIO pins connected to the encoders on the top two rows and the switch on the bottom row…
The encoders are ordered anti clock wise from the top Left…
So the
- first column are the Layer ( TL)
- second column Back (BL)
- third column Select ( BR)
- fourth column Learn (TR)
This is all very much he open source way of doing things. To properly support a zynhian infrastructure you can use a zynthian all in one board which does this over 12c bus, and then you will load up the settings in the webconf for that configuration which include numbers in the 100’s
IT may not seen particularly user friendly but it allows us to provide the same interface from similar devices delivered and presented in a zynthian like way.
The Offical kit does this all on the screen board so doesn’t need to support the flexibilities of a homebuild.
Looking forward to the 
The pictures of the installation often helps!