Hi Nathalia,
I’d cut holes in the wall where the windows are (you’d need to do that anyway, if you are going to use materials and a proper Render, so you can see inside).
If it is just a clay version and you are not going to do anything with it later, you could indeed just move the windows away from the walls a bit (won’t be considered best practice though, so better not show your .blend to another modeler…)
