There is no common WUE application. Some WUE institutions have their own WUE application posted. If they do not, make sure that you indicate you want to be considered for the WUE tuition rate somewhere on the application (whether it is online or a paper application).
Online education enrollment has continued to grow according to the new report, Digital Learning Compass: Digital Education Enrollment Report 2017. The overall enrollment in higher education, however, has fallen in the past three years.