The use of flexible endoscopes is the standard screening method for the upper gastrointestinal tract today. Disadvantages for the patient, due to the insertion process and often applied sedation, can be overcome with wireless capsule endoscopy (WCE). But WCE is not suited for the stomach as it can not guarantee a complete screening having no active guidance. With the magnetically guided capsule endoscopy (MGCE) a novel minimal invasive screening method for the gastrointestinal tract is being developed. With its current focus on the human stomach comes the need for a navigation and control method that is specialized for this application and its constraints. We present a new method for screening a waterfilled stomach with 10 functions for basic capsule movements, special maneuvers and mode-changes. Its evaluation was done in a clinical study consisting of 53 patient and volunteer cases. The individual evaluation of each function included a statistical analysis and an operators' survey. The functions proved sufficient to reach all parts of the stomach and to acquire close-up views of the mucosa.