Jimmy and Sheen enter Carl's body in order to get a virus' mitochondria so Jimmy can make a cure for the disease caused by the "get out of school sick" patches. In reality, this would make no sense, since viruses don't have mitochondria (though this was admittedly a genetically-engineered super virus).
Jimmy forgets that when someone is sick, the viruses don't exclusively inhabit the stomach. If anything, they are more concentrated in the bloodstream. Jimmy would have been better off drawing a sample of Carl's blood, saving him the effort of shrinking down and going inside him.