I assume the Flourite is on the bottom. With most plants that I plant, they are planted more than a inch deep so your plants will be fine. If you plant plants that only go in less than an inch, just mix the substrate where you plant. The roots will find there way to the Flourite. Also, most plant get there nutrients from the water column anyway. Amazon Swords I think like to get nutrients from the substrate but they will be planted deeper than an inch anyway. Also, nutrients from the water column will make it into the substrate.
Concerning the small rock that you mention, sometimes it is hard to keep some plants planted in this. I'd say, just plant and see what happens, If they grow well, then everything is fine, if not, than replant in the mixed substrate.
10 gallon hospital tank.
29 & 50 gallon - High Tech C02 enriched.
50 gallon Pond - Natural.