I will be shocked if your cories surivive your cycle. Did they know when they sold them to you that you were putting them into a brand new tank, especially one with amazonia in it? I'd consider returning them to your LFS and finishing your cycle without putting their lives at risk.
1.0ppm ammonia is way too high when you have fish in the tank. Higher than .25 starts to stress them out.. they might be "alive" now but they won't be for long especially as your ammonia levels continue to climb (you're at 2ppm on day 3, I expect they'll get much higher within the next week).
If you want to keep them you may end up doing water changes daily - and I'd suggest doing more than 40%.. you need to get that ammonia down to under .25ppm, and that would be difficult with a normal fish-in cycle, nevermind adding a substrate into the mix that is also adding ammonia to the cycle.