Zucchini is full of water. That combined with the liquid in the meat sauce can make for a watery dish. You can salt your zucchini boats and let them sit for 15 minutes to draw out the excess water. You can do this step before you start the meat sauce so they can sit while the sauce simmers. After 15 minutes, blot the zucchini with a paper towel. Another option is to place your zucchini on a baking rack while they cook so the water drips underneath. Use a short rack like a cookie cooling rack and place it in the baking dish or on a large pan. Then place the zucchini boats on top and carefully cover with the sauce. Bake following the recipe directions.