i just made something like this last week i used a large skillet i cooked my peppers and onions first till a little soft then i browned my hamburger and drained the fat put back in the skillet and added tomato sauce and a tps tomato paste and added chicken broth or water you want to be soupy so the macroni can cook i add uncook macroni in the skillet cover and cook untill the macroni is tender or you can cook the macroni seperate then add to meat mixture,in your case you want a casserole add everything in a casserole dish i remember my mom putting sour cream in it also about a tbs and yes you can put cheese on top matter of preference i don't usually bake it comes out great in the skillet for me.