Not quite the question you asked, but the most simple answer is that a cellar can easily be incorporated into the lowest level of the above ground building. Many castles I've visited had storage cellars, they were often simply built below the main floor which was accessed either by stairs, or from a different side. For example, look at the small windows below the arched windows of the Great Hall in Stirling Castle:

http://99percentinvisible.org/app/uploads/2015/08/Screen-Shot-2015-08-24-at-9.29.01-PM.png

Those represent a lower level, which can be accessed via the Outer Close (if I remember correctly. There are also stairs inside somewhere), whereas the actual hall is accessed from the Inner Close on the other side. The geography of the site allows this, and also the Inner Close plaza has obviously been flattened out, which involved the raising of the ground level.