Yes! Log your vitamins!
I have put my vitamins in under my custom foods. I take Amway vitamins (Nutrilite and Ocean Essentials) for the most part, and they are loaded with micronutrients. I found that when I compared my fitday nutrition log (average for two weeks) with the blood tests done at my doctor's office, the nutrition log was very accurate. I check my nutrition log at the end of the day--and it tells me if I need to take an extra supplement to reach my goal. The only one that consistently falls short is folic acid, I believe, because there is no way to enter it in the custom foods--and it is in my supplments AND in my protein shake powder.