If you have root heavy plants like Cryptocorynes or Echinodorus species, a plant soil under the substrate can really help with root growth as these are heavy root feeders. You can also place root tabs into the substrate where you would be planting for additional nutrients. However if you plan on having a lot of epiphyte plants such as Java Ferns, Anubias or Bucephalandra species then a soil substrate is somewhat wasted as these must not have the rhizomes covered and are suited to being attached to wood or rock. Stem plants use their roots to ground themselves well, but take most of their nutrients from the water column. So it really varies based on what you wish to plant! I personally love the Cryptocoryne species and have many of these in my plans so I always utilise a plant soil under my substrate.
RE having two types of substrate on the top layer, you can keep these separated by using rock to form a barrier between the two, as part of your scape. You can plug any gaps in the rock with fine filter wool then smaller rocks to hide the wool. That way, the rock forms a solid barrier between the two. There are some cool videos on the YouTube on how to do this.
