There are only three points of contact on a bicycle: the saddle, handlebars and of course the pedals. All three points are adjustable but the pedals are the most dynamic, and can be adjusted in five different parameters: fore/aft, rotation, medial/lateral, with wedges for foot biomechanics, and height for leg length discrepancies.
Getting all these adjustment correct can be complicated. It requires not only knowledge of equipment, but also the biomechanics of the human body. Most importantly, a proper fit process entails detailed communication and interaction between the cyclists and the fitter as to what feels the best. There is no automated fit process that can substitute experience or rider feedback and fitting is a dynamic process often taken in steps and stages.
Properly adjusted, the foot/pedal interface can prevent injury, increase power, and improve comfort; sometimes drastically. Yet, it is often the most overlooked or disregarded part of the fit process. Fitters and cyclists will often eyeball their cleat placement with little regard to proper placement.
But the adjustment process should include observation on the bike, analysis and measurement of biomechanics, installation, re-observation on the bike, and re-adjustment. This process in and of itself can take some time and even after the athlete has left the studio it may require slight adjustment after the cyclists puts some miles on the fit.
There are a great number of cycling shoe brands and models, each with their own engineering philosophy on how to make the "best" cycling shoe. There are about a half dozen popular brands of pedals with various cleat/pedal designs.
Starting with fore/aft adjustment we use the first and fifth metatarsal heads as our anatomical markers, or the two widest points of the forefoot. The center of the pedal spindle should be located between these two points with mechanical advantage of the plantar flexors towards the fifth (widest point at the outside of the forefoot). Many cleats have the center point of the cleat marked but some do not. I begin by marking the first and fifth metatarsal head on the shoe.