After spending a whole day doing all the routes and eater eggs, I have found the best way (in my opinion) to play this with all the routes and a headcanon.
SLIGHT SPOILER !!!!!!!!!!!!
It is best you do Alison's normal route AFTER you have done all 4 of the girls routes (making sure to save before the events). This way, Alison's secret hits harder and when you reload a save before Alison's ending you can play it off as an headcanon that the MC got some sort of time revers powers in order for a perfect ending. And this is where the Harem ending comes in.
In honesty, you can play it any way, I was just bored and Post Nut Clarity is stopping me from playing other games rn...