Hello and welcome abroad!
It’s your choice between defining this in Babylon or in the .glb, if you do in the .glb, it might be easier to place it wherever you want, as you could do that directly in your authoring tool 
As for managing, it’s also up to what works best for you, you could set a specific name for those surface/axis meshes and retrieve the meshes with scene.getMeshByName, or you could use custom .glb metadata: Custom GLB Metadata Workflow from 3dsMax - Demos and projects - Babylon.js (babylonjs.com)