Animal Crossing is a real time game in which things are very much progressed in 'one day at a time' measurements. The game will read your system time but it also has its own time. Is there any difference between changing the in-game time vs the system time to help go through the initial days? I am finding it common practice in this game to set your initial time back a bit to get through the tutorial sections faster so you can get into the game.
See my answer to Am I punished for playing with the game clock?; basically changing the game clock repeatedly is a very bad idea.
The game clock is basically an offset of your 3DS's system time. I would recommend leaving the game clock perfectly in sync with the system clock and altering the system clock if necessary, so you always know exactly what time it is in your Animal Crossing game by looking at/setting your 3DS clock.