Below I have set up an example of a proper toppings configuration for different sizes.
In the first image below I show I have 3 sizes for my pizzas. (small, medium, and large).
In this second image I have configured 3 different options. One option for 'Left Half Toppings', one for 'Right Half Toppings', and one for 'Whole Pizza Toppings'. Note the arrow pointing out the boxed checked for 'Prices Vary by Size'. Then below that I have selected 'Use Half/Half Toppings' and I proceeded to choose Main Topping option (whole), Left Side Topping Option (Left Half Toppings), and Right Side Toppings Option (Right Half Toppings)
In this third image I show the 'Whole Pizza Toppings' "Edit Values" display where it shows the 3 sizes and the prices for each topping. You will want to do this for all 3 option groups; whole, right & left.