If you are a retailer (as opposed to a restaurant owner) then variations of core products are made via variants. So if you currently have variations of your product, i.e. different sizes or colors of "Plaid Shirt," then you'll need to organize those variations as variants, not modifiers, in order to be reflected in Clover Online.
One reason for this is that the tracking of quantities is not available for modifiers, only variants. For more on variants, and how to set them, please visit this Clover support article.