So I'm trying to use auto-rig for my quadruped. I noticed on the parameter section (and on the tutorial from this site) that I'm supposed to provide a path for the Geometry in the Scene Object.

My question is, “should there only be ONE geometry node for a creature in Houdini?” I mean, should the body mesh and eye mesh be in the same geometry node?

it really depends on what your needs are…
having eyes in different objects allows for different rendering options etc…