If you look at this image of a plot I picked out in my own town, you can see that I've left patterns on my ground every two spaces, leaving no 3 by 3 areas for a house to plot, but the chosen area is a 3 by 3 plot. After that, I went around to my other spots I picked out, and put some patterns on them to prevent villagers from moving on those, meaning this is the only 'livable' spot in my town for my next villager to move onto.
Additionally, while a house is 3 by 3, the actual space of the house is 5 by 5, as they need an open area around the house for it to actually work. Basically, as long as you can dig a border around your chosen 3 by 3 spot, it should work.
As for "Plot Resetting", it is basically done by creating a new character/save file on your existing town, used to check if a house was plotted in the correct spot. Plots for villagers are only permanently set once the Mayor is loaded. If everything is acceptable, just save and quit on the new character, delete them, and then load your Mayor and you're A-OK.