I've prepared peppers stuffed with beef and rice a number of times, but they never turn out quite how I would like. How can should I cook the peppers so that they end up soft and flavorful, but are not overcooked to the point they are falling apart?
I pre-cook my peppers -- after I've cut them open, I let them roast in the oven for about 10-20 min, upside down (so they don't end up with a pool of water in the bottom). I then pull them out once they've softened up a little bit, fill them, and put them back in to warm through and melt any cheese, then switch it to broil to get them browned on top.
My filling is already cooked, as I typically use leftovers such as taco meat, rice & cheese. (my mom always insisted them were 'planned overs' as there are a number of dishes where we intentionally cook too much so that we'd have it as an ingredient for the next night's meal.)
When I've cooked stuffed peppers in the past, I typically cut the pepper length ways instead of just taking the top off. Once the filling has been added place tin foil over the dish for the first 15 minutes of the cooking time. This way, the peppers are allowed to soften a little through a steaming process and then allowed to gain colour during the remainder of the cooking process.
If you don't already, I'd also suggest pre-cooking the filling, this helps to reduce the overall cooking time and will help the peppers to retain their shape and not become overly soft.
I pre-cook the filling - it doesn't need to be cooked all the way, I usually just start the cooking process on the rice by putting in half the amount of water needed to fully cook it and letting it all boil out, before stirring the mince in to the hot rice - this is sufficient to bring the cooking time down enough that the peppers remain well formed and have a bit of bite to them, in a sufficiently hot oven.
I wrap each pepper individually in foil, and stand them up in the baking dish so as little as possible is touching the actual dish (I use small ramekins to stand them in).
I also pre-cook the filling.