He will get use to the sand.. Its kinda common for a ray not to like something new. If it has been use to a bare bottom tank, then you just add sand, he will kinda get stressed over it because its something new.
im not sure how much sand you added, but the best way to add sand to a ray tank this is use to being bare bottom is a little at a time.
Small amounts over a weeks time.
Put in just enough to kinda still see the bare bottom ,but still have sand.
then add in more
then more
cover half the tank with sand, then leave area on the other side low in sand..
Over the next week, slowly flatten it all out to were its all covered..
But since you didnt do that, just give it some time
Keep the lights off to reduce stress.
Maybe shift some of the sand over to the other side and have a bare area, lightly covered for him..
In time, the ray will get use to it..
As far as Ammonia in the tank. Ya, a little wont hurt rt now, but over time, the expos to the ammonia will weaken the health system of the ray and case problems.
Do a 30% to 40% water change.
This will help reduce your ammonia as well as get the ray to the bottom for a few min back on the sand...