That's fine, I do it all the time.
First of it helps to have at least two amiibo cards, since amiibo villagers take eons to ping, and it helps to have another card to kick them out with.
You use the genie lamp, if you're like me it's somewhere in your storage. You tap the card to either the bottom screen if you have a new 3ds or new 2ds xl or o the receiver if your ds diesn't have amiibo function. The wisp will ask you if you want to move that villager in or not. If you already have 10 villagers, you can choose who to kick out, if you have 9, they'll move in the next day.
To get them out, you choose that villager from the options when moving in a new amiibo and they'll be instantly in boxes.
If you choose the wrong one, you can quit without saving, so it might help the save and continue before you scan the card.
I hope I explained this well.