In feng shui terms, neglecting the state of your basement is neglecting the energy of your foundation. Scroll down to read the feng shui tips for your basement.
The fact that an area in your home, such as the basement, for example, is challenging, does not mean it has to have bad feng shui. It just means you have to spend a bit more time in creating (and keeping!) good feng shui energy in it.
I do not know the state of your basement - it might be still unfinished - but no matter what the case is, good feng shui means a clean space with fresh energy.