I asked because if you said soil, odds are it would be leeching nitrates and stuff into the water column. Since you're using Eco-Complete which is nothing more than clay, how much are dosing with the Thrive? The shrimp version of Thrive contains nitrogen, so using that wouldn't prevent nitrates from showing up in the water column. Don't stop dosing as you work through getting your tank straightened out, but try using only half of the suggested amount for a few weeks.
As it has already been pointed out, plants need nitrates and you control nitrates with water changes. As for what is causing the ammonia, swapping substrate will cause ammonia spikes as you removed all the bacteria in your old substrate that helps plants break things down as will rotting plant matter. Again, water changes and tank maintenance will help take care of those two issues.