William,
In THEORY, a layered substrate works but one of 2 things happens, inevitably:
1. You carefully don't clean all the way through the substrate in an attempt to not mix the two and disturb your 'look' or
2. You vigorously vacuum the substrate straight through to the bottom, attempting to get all the ditrius and debris out and mix the 2 substrates and then feel frustrated.
I can tell you this, I also used exactly these 2 products in tandem in a planted tank about 10 years ago--I had them completely mixed in a matter of a month or two.
Other comments I would like to extend to you:
3" thick substrate in total is deep and you would have to be impeccable in your maintenance to have a prayer of keeping the tank bacterial load from the substrate under wraps--it would eventually build up, esp if you are using pea gravel.
Gravel just allows too much space between particles, crap will find its way down there and the bacterial load will be a problem. the deeper the bed, the faster the problem will arise, IMO.
Plants do like the clay base but it is pretty dark in color and eventually also sort of turns to mush...
I would offer this, from my own experience: I pulled a 3" layer of said pea gravel and clay out of my tank, did a total breakdown and cleaning, and rescaped the tank with pool [silica] sand in a bed from 1-3" in depth. The plants root in it much more easily and prolifically, the crap stays mostly on the surface and can be easily vacuumed away. It is also an inert substrate, as are the 2 products you are talking about, so if this is to be a fully planted tank you will likely need both column and pellet type ferts, depending on the plants you choose to use.
Vacuuming pool sand is SO easy--the particles are heavy and do not easily suck up and away in your python if you watch what you are doing.
The sand is very clean and IME required very little initial cleaning--I dumped it all in to the tank and skipped the bucket in the bath tub ordeal, filled the tank and stirred vigorously, let the filters run for an hour or so [with clean prefilters on], vacuumed all the particulates then laying on the sand, and changed the water. It cleared in a couple hours--I began planting and the fish were in the tank that night.
The only caveat I want to extend is that with pool sand [and all other substrates, I think], you must also regularly vacuum to the full depth and move the sand around, or you will end up with pockets of anaerobic bacteria and that eventually will bite your fish in the butt.
I do one 75-80% water change weekly on my planted tank, vacuum thoroughly around the plants and sort of gently shake the crap from plant bases with the python--it's the best substrate I have ever used, or plan to, at this point!
Best regards,
Harriett