Since the betta is looking better, the meds must have worked the first time, even though it wasn't given in quite the right way! Don't worry about it; some med directions are confusing especially if you have to divide a dose. Just to make sure the betta is getting a good dose of the med, I would do a water change in the tank and give another 5-day dose.
This is how I used to dose for a small tank: If the directions say "x amount" for 10 gallons, then put that amount into a one gallon jug, like a clean, empty bottled water jug. Fill the jug with declorinated water first, add the med, and then shake to dissolve. For the first day dose, the dose is double strength for Maracyn. So you want to add about 3 cups of the medicine water to the water in his tank. On days 2-5, you'll add 1 1/2 cups of the medicine water to the tank. About every other day you'll have to remove 1 1/2 cups of tank water to make room for the new medicine water. After the last treatment, I would wait two days and do a water change of about 40-50%. Throw away the rest of the medicine water in the jug at the end of treatment - it won't stay potent for another treatment.