The custom log is basically a list of foods that don't show up in the fitday database (you have to enter the nutrition facts manually). It doesn't automatically add to your totals. When you eat one of these foods, you find it and add it to your daily list from the custom log section, rather than just typing it in on the main log page.
I use it for store-bought products, as (for example) the same type of cheese can be different in caloric ratios depending on the proportion of milk the manufacturer uses, etc. I got all the info for my entry off of the package.