Use the adjective methodological when you want to describe something that relates to the methods and practices of a certain discipline. As a doctor, you should always follow best methodological practices. If a patient has a headache, don't treat him for a sore foot or vice versa.
The roots of the adjective methodological can be broken into parts. Working backwards, -ical means "of or pertaining to," -ology means "branch of knowledge," and method is from both the Latin and Greek words methodus, meaning "a way of teaching or scientific inquiry." If you don't limit the variables, your research may have poor methodology. If you want to look at genes in blue-eyed people, but you study green-eyed people as well, you will have methodological problems.