When you have an item that has different pricing for a modifier, such as Frozen or Iced, the price change and setup for this is done directly on the item.
Above we see the Salted Caramel Waffle Latte has a Frozen cost of $1.50 for the large size, if that needs to change we have to login to Web Admin, in HQ Admin go into HQ Food & Drinks, Item Details, Items & Options. Below we can see that the search field helped find the item quicker.
Once you hit edit on that item, it brings up the list of options. We want to scroll down to the Variable Pricing section, and here we can see the Signature Drink Type. This section shows what the pricing is depending on the size of the drink and what option is selected.
The highlighted section shows the $1.50 price that is currently set. You can click on that price, and then change it to whatever fee is needed.
This process will need to be done on all items that are setup like this.