SPT files go into Documents\Adobe\Adobe Substance 3D Painter\assets\templates

You may have to create the templates folder.

SPEXP files go into Documents\Adobe\Adobe Substance 3D Painter\assets\export-presets

If installed correctly, when you go to start a new substance project, you will see the new FFXIV ____ Shader presets. 
Make sure you use the correct one for what you are working on.

When exporting textures, in the dropdown of which to choose, you should also see the new FFXIV ones.