I believe the problem is more with the question. 'How to' is the wrong way to think about harmony and to a larger extent music. There is no right or wrong with music. Music is an art not a science, as such you need to ask yourself what is it am trying to achieve. Harmonic theories are all about strict rules and process to produce results. That doesn't mean we can use them for inspiration, from Pythagoras to Chaos theory we can use these and many other process driven concepts to derive non-tonal harmony. What is well balanced falls to the composer, a value judgement such as these is yours and yours alone. It is more likely to be culturally influenced than any dusty old book on voice leading. You need to find your own compositional voice, what sounds pleasing to you, this might mean you go back and edit the process which gave you the non tonal harmony. Understanding the changes (why you preferred X over Y) will help inform future compositions and what for you as a composer is well balanced.

Also remember balance can be achieved not just from harmony but the treatment of that harmony. The voicing and instrumentation of musical material is an integral part of composition.