I have had that same "problem". I put dollops of the seasoned ricotta (I assume that what you're using?) along the edges of the filled stuffed- shell pan and cover with sauce and then bake. When serving, you can top each plate of stuffed shells with said dollop.
I also love ricotta on pizza... Layer tomato sauce, then a layer of filling, then mozzarella cheese; bake. Five minutes before done, remove from oven and sprinkle with parmesan, returning to oven to melt. Before serving, dollop more ricotta on top.
Cut a large round tomatoe in half and top each half with your leftover ricotta/mozz filling. Sprinkle with fresh basil or oregano and more mozz and toast in the toaster oven or broiler. Low fat, gets a veggie in your diet and use up that luscious filling