It could be the medicine is making him lethargic. Continue with the Maracyn Two until the end of its recommended dosing period unless your betta becomes worse in behavior. If the spots are healing, that's a good sign but if you stop medication too soon, bacterial infections can return and be resistant to treatment. So it's important not to stop unless necessary.
Hopefully your betta perks up after his treatment. If I am remembering correctly, he showed no signs of any internal problems, just the spots on his side and face, right? However, if he does have an internal problem such as an infection that is making him lethargic, the Maracyn Two should treat that as well because it absorbs well into the system. As long as the problem is not in the kidneys and your betta is not bloating, the medicine is safe to continue.