>>315797172
if you want symmetrical, it's easiest to set one half of the mesh as a different material that you're not going to use so the baking doesn't mess up.
to bake the high poly into the low poly, export them as separate files, drag the low poly into substance, and then add the high poly under "Bake Mesh Maps". 
after you've baked the maps, you can export a new lowpoly with only one material, and re-import to substance so you can see how it looks while you're working on it.