Either Don't cook the pasta - it's hard to tell you how much stock to put in doing it your way, or i cook the veg lightly, cook and drain the pasta well, make a roux based sauce, flour fat and perhaps milk, add herbs/garlic/cheese so it's quite thick, add pasta and veg, stir and sprinkle with a crushed packet of plain crisps mixed with some breadcrumbs and grated cheese for a lovely crispy top
As funnygirl has said make a cheese sauce,pre cook your pasta and cook veg until nearly cooked,mix through put in dish covered in cheese and breadceumbs,you could put some sliced tomatoes on top,bake in hot oven till top browned!
As others have said...you need to make a roux, and make a proper cream sauce - and add your cheese to that. Also-use full fat cheese. The way you did it,the fat free cheese broke down....and you ended up with a watery sauce.