I’ve done a few encoder to Pi implementations and there is a fairly detailed thread here…
The configuration is performed within the zynthian webconf and there is a mapping ( documented in the thread I believe
) that implements the choice of pins, but having said it’s all possible, I would consider using an allinone card as it avoids the wiring hell of a ribbon connector and all the soldering and plugs and sockets you inevitably end up with to make construction and testing viable.
I’ve never yet done one with the S1-S4 switches implemented and since, in my world, those are fairly important interface devices I tend to shy away from the GPIO approach. It can be a bit of a beast to maintain and I have moved at least one pin that seemed to fall foul of some upstream use as Pi’s evolved.
It is quite staggering what one can stick in a raspberry Pi 60W amp case!
For true zynthian historians on the linked thread there is the first semi acknowledgement that the audio out’s are reversed . . .