did you try my Script ? Advanced biped setup, by using this script u'll have two separate bone system, one with controls to animate that have multi root system, and one boundary rig that is simple bone chain and all the limbs are parented in hierarchy. most of the time people use nodes for controlling the rig and that can be the problem when you want to import the rig to game engine because the engine will not understand the nodes! so i suggest using my script, doing animation with control rig and then connect boundary to control and bake animation on the boundary and export it.