Since the word is you need an activated copy of a prior OS installed for an upgrade, I'm betting you will have to do a clean install. Even a upgrade using the custom option may not work because of the activation requirement. Maybe if you purchased the full edition and not an upgrade, you could use a valid key to activate the current install. But I do not know for sure about these types of details.
Considering some unauthorized software may have some little surprises in it, you might want to do a clean install using your newly purchased version just for safety sake. And this is all with the understanding you are talking about Ultimate.