So tomorrow one of my villagers will be in boxes naturally, but I will also be replacing a villager with an amiibo. Would it be alright if both were in boxes tomorrow, or can I wait for two days to invite the amiibo?
Don't worry, I once had Daisy and Diana in boxes at the same time. From my experience I would say that It is completely fine if they are in boxes at the same time.
Having two villagers in boxes is a bad idea. I may cause a glitch where only one villager will move out naturally. The other would have to be adopted or reset to move out by amiibo since they would not move out otherwise. So if this happens you may have to scan the amiibo again. I personally wait till the plot is free before you invite the amiibo