An integrated window structure having opposing substrates that sandwich an electrochromic coating, a dye layer and an ion-isolating mechanism. In some embodiments, this is a selective ion-conductive layer and other embodiments incorporate nanostructures and polymers to tether the dye ions; these methods prevent dye ions from transporting into the electrochromic layer during redox activity. Control and systems to integrate the electrochromic elements in windows is provided.