If you are trying to use NTR Helper for the initial seed, that is not needed anymore since PCalc can find the initial seed on its own. Just load the game with NTR without pressing anything.
Start up the game with NTR (Mode 3 if on O3DS), go to Festival Plaza, press X+Y to bring up NTR menu, enable debugger, then connect to internet and click on Connect in NTR Helper.
If you still haven't gotten it to work, make sure that the plugin folder is on root of the SD card. Inside the plugin folder should be the folders with the TitleIDs of the games, and then inside each of those folders a cheat.plg file. Also, make sure to use regular BootNTR and not mode 3.
Is your OR updated to the latest version? It should say 1.4 in bottom screen on top right when loading the game.
To be certain, you're pressing Start+Down to bring up the egg seed menu, and then pressing Select+Right and Select+Left to switch daycare views with the egg seed menu displayed?
I just tried using both plugins at once and the instant egg hatch cheat works along with PokeCalcNTR. I merged the two folders for each game together, updated BootNTR Selector, updated Sun/Moon, and then ingame activated the instant egg cheat. Works perfectly :)
PokeCalcNTR is a tool for RNGing legit Pokemon, and so modifications to the Pokemon will not be added to the plugin because that is not the intention of the usage of PokeCalcNTR.
However, there is a cheat plugin for Sun/Moon that includes instant egg hatch. Link...