If you go into the CK and look at the map for a house you buy, you will see that EVERYTHING is already placed. But most of it starts off as disabled.
Take Breezehome for example.
In the game when you first visit it after buying, there's junk piled around in corners, there's a usable bed upstairs and a chest. These are the only elements that start off as being enabled.
When you buy the bedroom package, assets associated with that package become enabled. Among those assets is a wall section with a door that divides the bedrooms (one for you and the other for your housecarl) from the rest of the loft area.
To do what you want, examine the interior that already exists for the house you want to add a basemant to. Create a new cell which would be the basemant itself. Add a door transition that leads to it and set it as disabled. Edit the list of things you can buy for the house in question and add "Basemant"
Make it so that, like the conditions that govern the other elements you buy, the door to the basemant becomes enabled when you buy the basemant.
Instead of a door, you could also use a trap door. All you need is an open area on the floor large enough to allow for it, and you can place it there.