A combination respiratory therapy management system creates a combined respiratory therapy prescription that can be executed by a combined respiratory therapy device to provide multiple coordinated respiratory therapies to a patient. The system can update the combined respiratory therapy prescription and implement the updates while the combined respiratory therapy device is in use. An integrated graphical user interface provides the patient and clinician with customization options and quick access to preselected operations of the combined respiratory therapy device. Additional features of the system enable remote access and control of the combination respiratory therapy device by remote clinicians.