I was just wondering if it was conceivable or even recommeneded to have the larger, more typical aquarium gravel on top of a healthy layer of substrate? Would this have an adverse affect on the plants?
I don't think it would hurt the plants. You can always experiment in a smaller tank if you want. Sand works really well to and I know that doesnt hurt the plants.
I assume you are talking about the colorful ceramic gravel sold at places like Pets Mart.
It won't hurt your plants nor fish. It is perfectly fine to do that. But, be careful when you unplant plants otherwise the root will carry the underlying substrate up and will look ugly. Also, you won't want to use gravel clearner for the same reason.
I've had trouble with larger gravel (5mm and larger pieces) in the past as it was difficult to plant in and sometimes damaged the stems of the stem plants. I also couldn't grow a carpet as the gravel size was too large for the plants to grow through easily. I switched over to a substrate with a smaller particle size (about 2-3 mm) and I'm never going back. However, if you just want a decorative area in part of the tank it shouldn't be a problem.