EAC monitors values that are stored client side and server side, if those do not add up it will reset them to server side and most likely flag you up at Ubisoft.
This cheat is for OFFLINE ONLY and your character/save (you have 3 available on PC) should only be used for that. If you want to play online, create a new character/save for your online adventures.
NEVER mix the two together.
You should be completely offline while using the trainer (Uplay) and all options for Multiplayer turned off.
Never use your hacked character save when online as it will most probably reset you back to normal.
From what I know EAC stores a ghost of your character stats that it syncs up with a cloud version of it, and if it becomes too different it flags you as a cheater.
[Edited by mrzoltowski, 11/30/2016 9:44:06 AM]
I highly doubt so since it's offline, they can't track but as the values are brought over to online play when you don't use the trainer, it might be counted in the leaderboards. To play safe, keep it offline for just that game if you are paranoid kind.