While you can create houses and buildings in the Toolkit using individual standalone elements (e.g. walls, floors, roofs, windows, etc), this is, in theory, more time-consuming than using the Constructions tool. I say “in theory,” because the Constructions tool is, in fact, the worst thing I’ve ever used. With that in mind, here are some tips!
To create doors or windows, click on a construction to select it, and go into tile mode by clicking the red brick wall icon in the sidebar.
Then click on a tile to select it, right-click, and choose “create door/window.” If you do not immediately see a door or window, that means you can’t create a door or a window here — either because the tile is not the correct size, or because the construction does not have doors or windows.