When you enter your vitamin as a food, you need to enter the number of milligrams. So for magnesium you would check the "info" link next to the nutrient (you can get there by clicking the CHANGE NUTRIENT GOALS link at the lower right hand side of the page). For magnesium you would see "Recommended daily intake: For men, 350 mg should be consumed daily, while women need 280 mg." So calculate 13% of that RDA for women and use that as your amount. After you have done that for all nutrients in your vitamin, click save. Now when you enter it in your food record it will add milligrams as with other foods.
Hope that helps. Let me know if you have any other questions I can help with.
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