No, putting sand on top of gravel willnot work, because the sand being smaller grain size will work its way down to the bottom with the gravel left on top. The only thing to do is change over the substrate completely, and at one go. The plants may be slightly set back, but I have moved plants around many times doing this or that, including changing all tank substrates to sand, and they quickly recover.
As for the ammonia and waste...obviously the waste is gone with the gravel. The substrate is the largest and most important bed for bacteria of many species, and this will be reduced but it quickly returns. You have plants so there should be no ammonia at all (that you can detect, or that will harm fish). Don't have the sand too deep; this partly depends upon the plants--for example, Echinodorus (swords) have extensive root systems and need space.
Argos Play Sand has been recommended by several UK members. Alternatively, you could get one of the aquarium river sands which are considerably more expensive but not problematic. Make sure it is inert (play sand is inert). Avoid pure black and pure white, both are problematic for fish.