Without an example of your custom CSS it is difficult to know exactly why it is not working as you want it to.
Harlowe 2.x defines it's default font-family using a CSS selector that targets the tw-story element like so.
font-family: "Georgia", "serif";
... so if you want your custom font-family to override the default then you need to add CSS to your story's Story Stylesheet area that targets the same tw-story element.
note: It is a good idea to always include a font hierarchy that ends in a generic family in case the desired font doesn't load or isn't available.
eg. font-family: "Diskontented", "Arial", "Sans-serif";