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. Some versions of the system provide additional features that allow the combined respiratory therapy prescriptions to be created, accessed, shared with other users, and performed by the combination respiratory therapy device in a customizable user-friendly and non-threatening way.