If that is Anubias
, and I can't tell from the photos, it shouldn't be in the gravel but attached to wood or rock; black cotton thread will work and be almost unnoticeable, or wedge the plant between two pieces of wood or rock; same as for Java Fern
, and it will take root in a few weeks and be attached. If these plants (I see one on the left and one on the far right) have a rhizome, a long thick "branch" from which arise the leaves, they are Anubias
Stem plants can be as deep as you like so long as they are held in the gravel. Roots will form from the stems under the gravel, and along the stems above gravel too.
Rosette plants like swords and Vallisneria having a root system attached to a white "crown" from which the leaves grow up should have the roots under the substrate but the crown must not be buried; at or slightly above the surface is fine.
Re the neons, true they are sensitive, but in a planted tank there is no cycle so this is not an issue. However, the water parameters may not be stable but provided there is not too extreme a fluctuation they should be OK. Tank raised fish are generally (but not always) less of a problem than their wild counterparts.