Change the snapping tool to Vertex (from the default Increment). Turn on snapping. Now the Mesh bones can be snapped to the balls on the ends of the Armature bones. Much easier than snapping the cursor to the armature, then snapping the Mesh to the Cursor.
Make sure to only move the bones in the beginning in edit mode, not object mode. If you did move it in object mode, make sure to apply position and scale on the armature (ctrl+A). Then re-generate the rig
