It's pretty complicated, since we don't have official support for itch client.
Either it saves the save files just like the regular game would (%APPDATA%\Roaming\RenPy\ACADEMY34-v0.2.3) or it saves them in some sort of special itch folder (%APPDATA%\itch\apps).
You can try downloading the latest public release without using the itch app and check if the game will automatically find the saves.