You may want to cook your zucchini boats ahead of time before adding any pizza sauce, cheese or toppings. Personally, I don't like my zucchini overdone and I like a little bit of firmness to them, especially when they are loaded with toppings. However, I recognize that everyone has different tastes and likes their veggies cooked in a different way. If you want them to be softer, bake them in the oven for 10-15 minutes before adding on your toppings.