You need to wire the encoders to the Geckos or you will not have closed loop to the drive, connecting the encoder to the SS will not give you closed loop.
The encoder inputs on the SS are I presume really meant for MPG input although I do have my spindle encoder going back there, for two reasons. One is the Index pulse is used for the spindle feedback to Mach and the second is in the hope that one day the spindle may have some sort of synchronising with the Z although I dont think it will as room is tight on the SS now.
Hood